******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme-suite.org . ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-sampled ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIV:434013-434511 1.0000 100 chrVII:148443-148769 1.0000 100 chrXII:951474-951687 1.0000 100 chrV:303061-303380 1.0000 100 chrX:121621-121721 1.0000 100 chrXII:728129-728630 1.0000 100 chrVI:157815-158170 1.0000 100 chrVII:736136-736598 1.0000 100 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chrXIII:892746-893270 1.0000 100 chrIV:386889-387172 1.0000 100 chrXII:605172-605579 1.0000 100 chrXII:930813-931184 1.0000 100 chrXVI:435723-436139 1.0000 100 chrXV:671066-671419 1.0000 100 chrVIII:160474-160998 1.0000 100 chrII:414030-414294 1.0000 100 chrXVI:576074-576408 1.0000 100 chrXV:978701-979225 1.0000 100 chrXII:510153-510677 1.0000 100 chrXVI:645282-645876 1.0000 100 chrIV:1434477-1435001 1.0000 100 chrXII:263092-263496 1.0000 100 chrXVI:817982-818117 1.0000 100 chrXII:5523-5787 1.0000 100 chrVII:107666-108190 1.0000 100 chrIV:340386-340599 1.0000 100 chrVII:255145-255509 1.0000 100 chrIV:1017038-1017445 1.0000 100 chrIV:1354956-1355201 1.0000 100 chrXI:284287-284738 1.0000 100 chrXII:708275-708493 1.0000 100 chrXI:617818-618342 1.0000 100 chrV:322032-322911 1.0000 100 chrVII:771979-772277 1.0000 100 chrXIV:414254-414593 1.0000 100 chrXVI:282272-282727 1.0000 100 chrI:142158-143530 1.0000 100 chrXIII:631907-632332 1.0000 100 chrXV:79685-80209 1.0000 100 chrV:124046-124570 1.0000 100 chrVII:478118-478642 1.0000 100 chrXII:1029782-1030096 1.0000 100 chrXIII:661707-662084 1.0000 100 chrXI:384849-385373 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 30 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 550 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 55000 N= 550 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.308 C 0.192 G 0.192 T 0.308 Background letter frequencies (from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background): A 0.311 C 0.189 G 0.189 T 0.311 ******************************************************************************** ******************************************************************************** MOTIF RAGGTYMKGGGTTCGABYCCC MEME-1 width = 21 sites = 34 llr = 661 E-value = 1.4e-109 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAGGTYMKGGGTTCGABYCCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 48132:6::1::::3a1::1: pos.-specific C ::::16422::::a::25a88 probability G 5287::1489a:::7:3:::2 matrix T ::1:74:4:1:aa:::35:1: bits 2.4 * * * 2.2 * * * 1.9 * * * 1.7 **** * * Relative 1.4 * ******** * * Entropy 1.2 ** * ******** *** (28.0 bits) 1.0 *** * ******** **** 0.7 ******* ******** **** 0.5 **************** **** 0.2 ********************* 0.0 --------------------- Multilevel GAGGTCAGGGGTTCGATCCCC consensus AG A TCT A GT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGGTYMKGGGTTCGABYCCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- chrIII:123440-123770 - 32 9.17e-13 TAGGGTGCGG GAGGTCCCGGGTTCGAGTCCC GGCTCGCCCC chrXVI:581886-582298 + 62 2.53e-12 TCTTAATCAT AAGGTTAGGGGTTCGAGCCCC CTACAGGGCT chrVII:122141-122487 + 47 2.53e-12 TCTTAATCAT AAGGTTAGGGGTTCGAGCCCC CTACAGGGCT chrVII:185580-185943 - 13 2.53e-12 TCTTAATCAT AAGGTTAGGGGTTCGAGCCCC CTACAGGGCT chrV:135230-135678 - 31 2.53e-12 TCTTAATCAT AAGGTTAGGGGTTCGAGCCCC CTACAGGGCT chrVI:226525-226904 - 34 2.53e-12 TCTTAATCAT AAGGTTAGGGGTTCGAGCCCC CTACAGGGCT chrVII:876247-876692 + 17 2.53e-12 TCTTAATCAT AAGGTTAGGGGTTCGAGCCCC CTACAGGGCT chrXVI:769032-769500 - 1 4.90e-11 AGGATACCGA AATGTCAGGGGTTCGAGCCCC chrVII:115351-115743 + 56 4.90e-11 AGGATACCGA AATGTCAGGGGTTCGAGCCCC CTATGAGGAG chrVII:828528-828985 - 27 6.27e-11 TTCTAATCAG AAGATTATGGGTTCGACCCCC ATCGTGAGTG chrIV:568708-569135 + 52 6.27e-11 TTCTAATCAG AAGATTATGGGTTCGACCCCC ATCGTGAGTG chrXI:162354-162727 - 7 6.27e-11 TTCTAATCAG AAGATTATGGGTTCGACCCCC ATCGTG chrVII:736136-736598 + 64 6.27e-11 TTCTAATCAG AAGATTATGGGTTCGACCCCC ATCGTGAGTG chrXIV:567948-568389 + 69 1.01e-10 AAGCATGCGA GAGGCCCTGGGTTCAATTCCC AGCTCGCCCC chrXIV:567948-568377 + 75 1.01e-10 AAGCATGCGA GAGGCCCTGGGTTCAATTCCC AGCTC chrXV:464261-464837 + 22 1.01e-10 AAGCATGCGA GAGGCCCTGGGTTCAATTCCC AGCTCGCCCC chrIV:1017038-1017445 - 26 2.97e-10 TTCTCACCGT GGAGACCGGGGTTCGACTCCC CGCTTCGGAG chrVII:328430-328887 + 16 2.97e-10 CTTTCACCGT GGAGACCGGGGTTCGACTCCC CGTATCGGAG chrXII:797018-797367 + 77 2.97e-10 CTTTCACCGT GGAGACCGGGGTTCGACTCCC CGT chrXII:1051994-1052262 - 3 4.47e-10 TAATAACGCG GGGATCAGCGGTTCGATCCCG CT chrVII:779470-779796 + 74 9.55e-10 CTTCCAAGGT GGGGACACGGGTTCGATTCTC GTACCG chrXIV:96118-96462 - 11 9.55e-10 CTTCCAAGGT GGGGACACGGGTTCGATTCTC GTACCGCTCA chrVIII:358341-358711 - 12 1.93e-09 AAGTTATCTG GAGGTCCTGTGTTCGATCCAC AGAATTCGCA chrVII:440519-441019 - 7 1.93e-09 AAGTTATCTG GAGGTCCTGTGTTCGATCCAC AGAATT chrIV:1075347-1075709 - 4 2.28e-09 TCACACGGCA AAGGTCCCGAGTTCGATCCTC GGT chrXV:113639-113995 + 77 4.66e-09 TAGTAATGTG GAGATCATCGGTTCAAATCCG ATT chrVIII:115921-116370 - 22 4.66e-09 TAGTAATGTG GAGATCATCGGTTCAAATCCG ATTGGAAGCA chrXIV:560551-560935 - 10 4.66e-09 TAGTAATGTG GAGATCATCGGTTCAAATCCG ATTGGAAGC chrIV:434013-434511 - 62 4.66e-09 TAGTAATGTG GAGATCATCGGTTCAAATCCG ATTGGAAGCA chrIV:83416-83714 + 73 1.87e-08 TTGCCATCGT TGGGCCCCCGGTTCGATTCCG GGCTTGC chrXIII:168646-169006 + 77 2.12e-08 ACGAAATCTT GAGATCGGGCGTTCGACTCGC CCC chrX:422776-422876 + 75 6.31e-08 TCATAATCTG AAGGTCGAGAGTTCGAACCTC CCCTG chrVII:544427-544828 - 10 9.01e-08 TTGTCGCGTG CCAGATCGGGGTTCAATTCCC CGTCGCGGA chrXII:374174-374605 + 58 1.15e-07 TACGAACCAG AAGATTCCAGGTTCAAGTCCT GGCGGGGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGGTYMKGGGTTCGABYCCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:123440-123770 9.2e-13 31_[-1]_48 chrXVI:581886-582298 2.5e-12 61_[+1]_18 chrVII:122141-122487 2.5e-12 46_[+1]_33 chrVII:185580-185943 2.5e-12 12_[-1]_67 chrV:135230-135678 2.5e-12 30_[-1]_49 chrVI:226525-226904 2.5e-12 33_[-1]_46 chrVII:876247-876692 2.5e-12 16_[+1]_63 chrXVI:769032-769500 4.9e-11 [-1]_79 chrVII:115351-115743 4.9e-11 55_[+1]_24 chrVII:828528-828985 6.3e-11 26_[-1]_53 chrIV:568708-569135 6.3e-11 51_[+1]_28 chrXI:162354-162727 6.3e-11 6_[-1]_73 chrVII:736136-736598 6.3e-11 63_[+1]_16 chrXIV:567948-568389 1e-10 68_[+1]_11 chrXIV:567948-568377 1e-10 74_[+1]_5 chrXV:464261-464837 1e-10 21_[+1]_58 chrIV:1017038-1017445 3e-10 25_[-1]_54 chrVII:328430-328887 3e-10 15_[+1]_64 chrXII:797018-797367 3e-10 76_[+1]_3 chrXII:1051994-1052262 4.5e-10 2_[-1]_77 chrVII:779470-779796 9.6e-10 73_[+1]_6 chrXIV:96118-96462 9.6e-10 10_[-1]_69 chrVIII:358341-358711 1.9e-09 11_[-1]_68 chrVII:440519-441019 1.9e-09 6_[-1]_73 chrIV:1075347-1075709 2.3e-09 3_[-1]_76 chrXV:113639-113995 4.7e-09 76_[+1]_3 chrVIII:115921-116370 4.7e-09 21_[-1]_58 chrXIV:560551-560935 4.7e-09 9_[-1]_70 chrIV:434013-434511 4.7e-09 61_[-1]_18 chrIV:83416-83714 1.9e-08 72_[+1]_7 chrXIII:168646-169006 2.1e-08 76_[+1]_3 chrX:422776-422876 6.3e-08 74_[+1]_5 chrVII:544427-544828 9e-08 9_[-1]_70 chrXII:374174-374605 1.1e-07 57_[+1]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGGTYMKGGGTTCGABYCCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAGGTYMKGGGTTCGABYCCC width=21 seqs=34 chrIII:123440-123770 ( 32) GAGGTCCCGGGTTCGAGTCCC 1 chrXVI:581886-582298 ( 62) AAGGTTAGGGGTTCGAGCCCC 1 chrVII:122141-122487 ( 47) AAGGTTAGGGGTTCGAGCCCC 1 chrVII:185580-185943 ( 13) AAGGTTAGGGGTTCGAGCCCC 1 chrV:135230-135678 ( 31) AAGGTTAGGGGTTCGAGCCCC 1 chrVI:226525-226904 ( 34) AAGGTTAGGGGTTCGAGCCCC 1 chrVII:876247-876692 ( 17) AAGGTTAGGGGTTCGAGCCCC 1 chrXVI:769032-769500 ( 1) AATGTCAGGGGTTCGAGCCCC 1 chrVII:115351-115743 ( 56) AATGTCAGGGGTTCGAGCCCC 1 chrVII:828528-828985 ( 27) AAGATTATGGGTTCGACCCCC 1 chrIV:568708-569135 ( 52) AAGATTATGGGTTCGACCCCC 1 chrXI:162354-162727 ( 7) AAGATTATGGGTTCGACCCCC 1 chrVII:736136-736598 ( 64) AAGATTATGGGTTCGACCCCC 1 chrXIV:567948-568389 ( 69) GAGGCCCTGGGTTCAATTCCC 1 chrXIV:567948-568377 ( 75) GAGGCCCTGGGTTCAATTCCC 1 chrXV:464261-464837 ( 22) GAGGCCCTGGGTTCAATTCCC 1 chrIV:1017038-1017445 ( 26) GGAGACCGGGGTTCGACTCCC 1 chrVII:328430-328887 ( 16) GGAGACCGGGGTTCGACTCCC 1 chrXII:797018-797367 ( 77) GGAGACCGGGGTTCGACTCCC 1 chrXII:1051994-1052262 ( 3) GGGATCAGCGGTTCGATCCCG 1 chrVII:779470-779796 ( 74) GGGGACACGGGTTCGATTCTC 1 chrXIV:96118-96462 ( 11) GGGGACACGGGTTCGATTCTC 1 chrVIII:358341-358711 ( 12) GAGGTCCTGTGTTCGATCCAC 1 chrVII:440519-441019 ( 7) GAGGTCCTGTGTTCGATCCAC 1 chrIV:1075347-1075709 ( 4) AAGGTCCCGAGTTCGATCCTC 1 chrXV:113639-113995 ( 77) GAGATCATCGGTTCAAATCCG 1 chrVIII:115921-116370 ( 22) GAGATCATCGGTTCAAATCCG 1 chrXIV:560551-560935 ( 10) GAGATCATCGGTTCAAATCCG 1 chrIV:434013-434511 ( 62) GAGATCATCGGTTCAAATCCG 1 chrIV:83416-83714 ( 73) TGGGCCCCCGGTTCGATTCCG 1 chrXIII:168646-169006 ( 77) GAGATCGGGCGTTCGACTCGC 1 chrX:422776-422876 ( 75) AAGGTCGAGAGTTCGAACCTC 1 chrVII:544427-544828 ( 10) CCAGATCGGGGTTCAATTCCC 1 chrXII:374174-374605 ( 58) AAGATTCCAGGTTCAAGTCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGGTYMKGGGTTCGABYCCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 44000 bayes= 11.7023 E= 1.4e-109 50 -268 140 -340 130 -268 12 -1173 -140 -1173 212 -240 6 -1173 184 -1173 -82 -68 -1173 118 -1173 177 -1173 18 85 102 -168 -1173 -340 -10 112 30 -340 -10 207 -1173 -240 -268 217 -240 -1173 -1173 240 -1173 -1173 -1173 -1173 169 -1173 -1173 -1173 169 -1173 240 -1173 -1173 -23 -1173 196 -1173 169 -1173 -1173 -1173 -108 32 64 6 -1173 140 -1173 69 -1173 240 -1173 -1173 -240 207 -268 -140 -1173 207 -10 -340 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGGTYMKGGGTTCGABYCCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 34 E= 1.4e-109 0.441176 0.029412 0.500000 0.029412 0.764706 0.029412 0.205882 0.000000 0.117647 0.000000 0.823529 0.058824 0.323529 0.000000 0.676471 0.000000 0.176471 0.117647 0.000000 0.705882 0.000000 0.647059 0.000000 0.352941 0.558824 0.382353 0.058824 0.000000 0.029412 0.176471 0.411765 0.382353 0.029412 0.176471 0.794118 0.000000 0.058824 0.029412 0.852941 0.058824 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.264706 0.000000 0.735294 0.000000 1.000000 0.000000 0.000000 0.000000 0.147059 0.235294 0.294118 0.323529 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.058824 0.794118 0.029412 0.117647 0.000000 0.794118 0.176471 0.029412 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGGTYMKGGGTTCGABYCCC MEME-1 regular expression -------------------------------------------------------------------------------- [GA][AG]G[GA]T[CT][AC][GT]GGGTTC[GA]A[TGC][CT]CCC -------------------------------------------------------------------------------- Time 295.85 secs. ******************************************************************************** ******************************************************************************** MOTIF SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 width = 25 sites = 56 llr = 980 E-value = 1.6e-161 ******************************************************************************** -------------------------------------------------------------------------------- Motif SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 Description -------------------------------------------------------------------------------- Simplified A :111:464:39::322::a443431 pos.-specific C 53924:16a4:9:22:a8:413135 probability G 56:21:1::21::468::::32434 matrix T :::6662::::1a1:::2:1121:1 bits 2.4 * * 2.2 * * 1.9 * * 1.7 * * ** *** Relative 1.4 * * ** **** Entropy 1.2 *** * *** **** (25.2 bits) 1.0 *** ** *** ***** 0.7 *** ** ** *** ***** * 0.5 *** ** ****** ****** ** 0.2 ********************* *** 0.0 ------------------------- Multilevel CGCTTTACCCACTGGGCCAAAAACC consensus GC CA A A AAA CGCGAG sequence G C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------- chrVII:738965-739299 - 41 1.30e-11 TTAGCACGGT GCCTTAACCAACTGGGCCAAGAGAC CTATTTTTTT chrV:443112-443456 + 16 1.30e-11 TTAGCACGGT GCCTTAACCAACTGGGCCAAGAGAC CAAATTTTAA chrXII:1051994-1052262 + 41 1.30e-11 TTAGCACGGT GCCTTAACCAACTGGGCCAAGAGAC CATGAAAAGG chrXII:656857-657139 + 33 2.28e-11 GCTAAGGGAG CGCGCTACCGACTACGCCACACGCC CAATTTTCTT chrXVI:856700-857111 - 48 2.28e-11 GCTAAGGGAG CGCGCTACCGACTACGCCACACGCC CGAATCTTGT chrXI:517818-518172 - 44 2.28e-11 GCTAAGGGAG CGCGCTACCGACTACGCCACACGCC CATAGTAGAT chrX:617752-617852 - 28 8.80e-11 TAAATCTGAC GCCTTAAACCACTCGGCCAAACTCC CATTGTTTGT chrXII:731916-732363 - 2 8.80e-11 TAAATCTGAC GCCTTAAACCACTCGGCCAAACTCC C chrXII:592407-592795 + 43 8.80e-11 TAAATCTGAC GCCTTAAACCACTCGGCCAAACTCC CATTGTATGT chrII:226904-227288 - 30 1.20e-10 TCTAATCTTT CGCCTTAACCACTCGGCCAAGTTGC CTCGTTTTAC chrIV:437611-437947 - 44 1.20e-10 TCTAATCTTT CGCCTTAACCACTCGGCCAAGTTGC CTTACTAATG chrIV:1305459-1305826 - 39 1.20e-10 TCTAATCTTT CGCCTTAACCACTCGGCCAAGTTGC CTTAATTTGT chrI:166065-166482 - 45 2.86e-10 GCAAGGGAAG CGCGCTACCAACTGCGCCATGTGCC CAACTCATTA chrIII:227755-228179 - 26 4.90e-10 TCGAGTCTCT CGCCTTAACCACTCGGCCATAGTGC CATTTCGATT chrXV:274518-274904 - 13 9.22e-10 AGCAGGGCAT CGCCTTAACCACTCGGCCACTGGGA CACGATTACT chrXVI:769032-769500 + 61 1.48e-09 AAAAGCCGAA CGCTCTACCAACTGAGCTAACAAGG ATGAGTTCTT chrXV:438443-438907 - 19 1.48e-09 AAAAGCCGAA CGCTCTACCAACTGAGCTAACAAGG ATGAGTTCTT chrXV:113639-113995 - 36 1.67e-09 ACTAGTGTGG CGCCTTACCAACTTGGCCATAGAAG CTAAATCTCT chrVII:857281-857603 + 74 1.67e-09 TGAATCAGGC GCCTTAGACCGCTCGGCCAAACAAC CA chrVII:205400-205714 - 15 1.67e-09 TGAATCAGGC GCCTTAGACCGCTCGGCCAAACAAC CACTTATTTG chrVIII:115921-116370 + 59 1.67e-09 ACTAGTGTGG CGCCTTACCAACTTGGCCATAGAAG CTCTAATAGT chrIV:1461583-1462013 + 56 1.67e-09 TGAATCAGGC GCCTTAGACCGCTCGGCCAAACAAC CACTTATTTG chrXIII:504710-505115 - 34 1.67e-09 TGAATCAGGC GCCTTAGACCGCTCGGCCAAACAAC CACTTATCTG chrXIV:560551-560935 + 47 1.67e-09 ACTAGTGTGG CGCCTTACCAACTTGGCCATAGAAG CCCGTTATTA chrXVI:581886-582298 - 21 2.60e-09 AAGAGTCATA CGCGCTACCGATTGCGCCAACAAGG CTCTTTTGTT chrVII:122141-122487 - 6 2.60e-09 AAGAGTCATA CGCGCTACCGATTGCGCCAACAAGG CTAAT chrXIII:372391-372680 + 8 2.60e-09 AGCAGAT GCCATAACCGACTAGACCACGAAAC CAGGTTTTAT chrVII:185580-185943 + 50 2.60e-09 AAGAGTCATA CGCGCTACCGATTGCGCCAACAAGG CTATTTCGTT chrXI:308046-308375 + 32 2.60e-09 TTAAGCAGAT GCCATAACCGACTAGACCACGAAAC CACTTAATTG chrV:135230-135678 + 68 2.60e-09 AAGAGTCATA CGCGCTACCGATTGCGCCAACAAGG CTTTTTTC chrVII:823306-823674 - 43 2.60e-09 TTAAGCAGAT GCCATAACCGACTAGACCACGAAAC CACTCTTATT chrV:438544-438863 - 48 2.60e-09 TTAAGCAGAT GCCATAACCGACTAGACCACGAAAC CTAATTTGTT chrVI:226525-226904 + 71 2.60e-09 AAGAGTCATA CGCGCTACCGATTGCGCCAACAAGG CATTT chrX:378204-378304 - 60 2.60e-09 TTAAGCAGAT GCCATAACCGACTAGACCACGAAAC CTATTAATTT chrIII:127547-127909 - 39 1.39e-08 ACAGTCGCAC GCCTTAACCAACTTGGCCATGGAGT CATTTTATCT chrVII:730962-731323 - 46 1.39e-08 ACAGTCGCAC GCCTTAACCAACTTGGCCATGGAGT CTTTTTGACT chrXIV:102553-102893 - 44 1.39e-08 ACAGTCGCAC GCCTTAACCAACTTGGCCATGGAGT CTTATAATAT chrIV:884181-884628 - 8 1.52e-08 ATAAGCACGA AGCTCTAACCACTGAGCTACACGAG CATTTTC chrVIII:358341-358711 + 68 1.66e-08 TTCAGTCTGG CGCTCTCCCAACTGAGCTAAATCCG CTTACTAT chrII:36270-36571 - 29 1.66e-08 TTCAGTCTGG CGCTCTCCCAACTGAGCTAAATCCG CTTACAACTA chrVII:440519-441019 + 63 1.66e-08 TTCAGTCTGG CGCTCTCCCAACTGAGCTAAATCCG CATATATTTT chrVI:157815-158170 + 40 1.66e-08 TTCAGTCTGG CGCTCTCCCAACTGAGCTAAATCCG CTTCTATTTA chrV:492205-492620 + 37 1.82e-08 CGTAGCCAGA CGCCGTGACCATTGGGCCACGAGGA ATAGGATGTT chrXI:490831-491122 - 43 1.82e-08 CGTAGCCAGA CGCCGTGACCATTGGGCCACGAGGA ACAAGAATTA chrXII:374174-374605 - 17 1.82e-08 CGTAGCCAGA CGCCGTGACCATTGGGCCACGAGGA ACAAGATTTA chrXII:962892-963217 + 26 1.82e-08 TAAGTCTGCC GCCTTAGACCACTCGGCCAACCCTC CGTCGATAAT chrXIV:567948-568377 - 4 3.00e-08 CCCAAAGCGA GAATCATACCACTAGACCACACGCC CGA chrXII:92367-92779 - 26 3.00e-08 CCCAAAGCGA GAATCATACCACTAGACCACACGCC CTTATTAACT chrX:390902-391002 + 36 6.02e-08 ATGAGACTGA CGCTCTTCCTACTGAGCTACTGAAG CACTATTTCT chrX:422776-422876 - 34 6.02e-08 ATGAGACTGA CGCTCTTCCTACTGAGCTACTGAAG CATACAAAGG chrIII:142597-142929 + 33 6.47e-08 TGGCAACGTT GGATTTTACCACTAAACCACTTGCG CTAGTAATCT chrXVI:860210-860554 - 48 6.47e-08 TGGCAACGTT GGATTTTACCACTAAACCACTTGCG CTTGTTATTT chrIV:83416-83714 - 34 6.47e-08 TGGCAACGTT GGATTTTACCACTAAACCACTTGCG CTAAGTGAAC chrVI:162068-162379 - 56 6.47e-08 TGGCAACGTT GGATTTTACCACTAAACCACTTGCG CTTGTTTTCT chrXV:980517-980929 - 11 2.55e-07 CCCAAAGCGA GAATCATTCCACTAGACCACACGCC CATACAATTT chrIII:123440-123770 + 68 3.79e-07 CCCTAAGCGA GAATCATACCTCTAGACCACACGCC CTCCTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrVII:738965-739299 1.3e-11 40_[-2]_35 chrV:443112-443456 1.3e-11 15_[+2]_60 chrXII:1051994-1052262 1.3e-11 40_[+2]_35 chrXII:656857-657139 2.3e-11 32_[+2]_43 chrXVI:856700-857111 2.3e-11 47_[-2]_28 chrXI:517818-518172 2.3e-11 43_[-2]_32 chrX:617752-617852 8.8e-11 27_[-2]_48 chrXII:731916-732363 8.8e-11 1_[-2]_74 chrXII:592407-592795 8.8e-11 42_[+2]_33 chrII:226904-227288 1.2e-10 29_[-2]_46 chrIV:437611-437947 1.2e-10 43_[-2]_32 chrIV:1305459-1305826 1.2e-10 38_[-2]_37 chrI:166065-166482 2.9e-10 44_[-2]_31 chrIII:227755-228179 4.9e-10 25_[-2]_50 chrXV:274518-274904 9.2e-10 12_[-2]_63 chrXVI:769032-769500 1.5e-09 60_[+2]_15 chrXV:438443-438907 1.5e-09 18_[-2]_57 chrXV:113639-113995 1.7e-09 35_[-2]_40 chrVII:857281-857603 1.7e-09 73_[+2]_2 chrVII:205400-205714 1.7e-09 14_[-2]_61 chrVIII:115921-116370 1.7e-09 58_[+2]_17 chrIV:1461583-1462013 1.7e-09 55_[+2]_20 chrXIII:504710-505115 1.7e-09 33_[-2]_42 chrXIV:560551-560935 1.7e-09 46_[+2]_29 chrXVI:581886-582298 2.6e-09 20_[-2]_55 chrVII:122141-122487 2.6e-09 5_[-2]_70 chrXIII:372391-372680 2.6e-09 7_[+2]_68 chrVII:185580-185943 2.6e-09 49_[+2]_26 chrXI:308046-308375 2.6e-09 31_[+2]_44 chrV:135230-135678 2.6e-09 67_[+2]_8 chrVII:823306-823674 2.6e-09 42_[-2]_33 chrV:438544-438863 2.6e-09 47_[-2]_28 chrVI:226525-226904 2.6e-09 70_[+2]_5 chrX:378204-378304 2.6e-09 59_[-2]_16 chrIII:127547-127909 1.4e-08 38_[-2]_37 chrVII:730962-731323 1.4e-08 45_[-2]_30 chrXIV:102553-102893 1.4e-08 43_[-2]_32 chrIV:884181-884628 1.5e-08 7_[-2]_68 chrVIII:358341-358711 1.7e-08 67_[+2]_8 chrII:36270-36571 1.7e-08 28_[-2]_47 chrVII:440519-441019 1.7e-08 62_[+2]_13 chrVI:157815-158170 1.7e-08 39_[+2]_36 chrV:492205-492620 1.8e-08 36_[+2]_39 chrXI:490831-491122 1.8e-08 42_[-2]_33 chrXII:374174-374605 1.8e-08 16_[-2]_59 chrXII:962892-963217 1.8e-08 25_[+2]_50 chrXIV:567948-568377 3e-08 3_[-2]_72 chrXII:92367-92779 3e-08 25_[-2]_50 chrX:390902-391002 6e-08 35_[+2]_40 chrX:422776-422876 6e-08 33_[-2]_42 chrIII:142597-142929 6.5e-08 32_[+2]_43 chrXVI:860210-860554 6.5e-08 47_[-2]_28 chrIV:83416-83714 6.5e-08 33_[-2]_42 chrVI:162068-162379 6.5e-08 55_[-2]_20 chrXV:980517-980929 2.6e-07 10_[-2]_65 chrIII:123440-123770 3.8e-07 67_[+2]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SSCTYWAMCVACTVGGCCAMRNRVS width=25 seqs=56 chrVII:738965-739299 ( 41) GCCTTAACCAACTGGGCCAAGAGAC 1 chrV:443112-443456 ( 16) GCCTTAACCAACTGGGCCAAGAGAC 1 chrXII:1051994-1052262 ( 41) GCCTTAACCAACTGGGCCAAGAGAC 1 chrXII:656857-657139 ( 33) CGCGCTACCGACTACGCCACACGCC 1 chrXVI:856700-857111 ( 48) CGCGCTACCGACTACGCCACACGCC 1 chrXI:517818-518172 ( 44) CGCGCTACCGACTACGCCACACGCC 1 chrX:617752-617852 ( 28) GCCTTAAACCACTCGGCCAAACTCC 1 chrXII:731916-732363 ( 2) GCCTTAAACCACTCGGCCAAACTCC 1 chrXII:592407-592795 ( 43) GCCTTAAACCACTCGGCCAAACTCC 1 chrII:226904-227288 ( 30) CGCCTTAACCACTCGGCCAAGTTGC 1 chrIV:437611-437947 ( 44) CGCCTTAACCACTCGGCCAAGTTGC 1 chrIV:1305459-1305826 ( 39) CGCCTTAACCACTCGGCCAAGTTGC 1 chrI:166065-166482 ( 45) CGCGCTACCAACTGCGCCATGTGCC 1 chrIII:227755-228179 ( 26) CGCCTTAACCACTCGGCCATAGTGC 1 chrXV:274518-274904 ( 13) CGCCTTAACCACTCGGCCACTGGGA 1 chrXVI:769032-769500 ( 61) CGCTCTACCAACTGAGCTAACAAGG 1 chrXV:438443-438907 ( 19) CGCTCTACCAACTGAGCTAACAAGG 1 chrXV:113639-113995 ( 36) CGCCTTACCAACTTGGCCATAGAAG 1 chrVII:857281-857603 ( 74) GCCTTAGACCGCTCGGCCAAACAAC 1 chrVII:205400-205714 ( 15) GCCTTAGACCGCTCGGCCAAACAAC 1 chrVIII:115921-116370 ( 59) CGCCTTACCAACTTGGCCATAGAAG 1 chrIV:1461583-1462013 ( 56) GCCTTAGACCGCTCGGCCAAACAAC 1 chrXIII:504710-505115 ( 34) GCCTTAGACCGCTCGGCCAAACAAC 1 chrXIV:560551-560935 ( 47) CGCCTTACCAACTTGGCCATAGAAG 1 chrXVI:581886-582298 ( 21) CGCGCTACCGATTGCGCCAACAAGG 1 chrVII:122141-122487 ( 6) CGCGCTACCGATTGCGCCAACAAGG 1 chrXIII:372391-372680 ( 8) GCCATAACCGACTAGACCACGAAAC 1 chrVII:185580-185943 ( 50) CGCGCTACCGATTGCGCCAACAAGG 1 chrXI:308046-308375 ( 32) GCCATAACCGACTAGACCACGAAAC 1 chrV:135230-135678 ( 68) CGCGCTACCGATTGCGCCAACAAGG 1 chrVII:823306-823674 ( 43) GCCATAACCGACTAGACCACGAAAC 1 chrV:438544-438863 ( 48) GCCATAACCGACTAGACCACGAAAC 1 chrVI:226525-226904 ( 71) CGCGCTACCGATTGCGCCAACAAGG 1 chrX:378204-378304 ( 60) GCCATAACCGACTAGACCACGAAAC 1 chrIII:127547-127909 ( 39) GCCTTAACCAACTTGGCCATGGAGT 1 chrVII:730962-731323 ( 46) GCCTTAACCAACTTGGCCATGGAGT 1 chrXIV:102553-102893 ( 44) GCCTTAACCAACTTGGCCATGGAGT 1 chrIV:884181-884628 ( 8) AGCTCTAACCACTGAGCTACACGAG 1 chrVIII:358341-358711 ( 68) CGCTCTCCCAACTGAGCTAAATCCG 1 chrII:36270-36571 ( 29) CGCTCTCCCAACTGAGCTAAATCCG 1 chrVII:440519-441019 ( 63) CGCTCTCCCAACTGAGCTAAATCCG 1 chrVI:157815-158170 ( 40) CGCTCTCCCAACTGAGCTAAATCCG 1 chrV:492205-492620 ( 37) CGCCGTGACCATTGGGCCACGAGGA 1 chrXI:490831-491122 ( 43) CGCCGTGACCATTGGGCCACGAGGA 1 chrXII:374174-374605 ( 17) CGCCGTGACCATTGGGCCACGAGGA 1 chrXII:962892-963217 ( 26) GCCTTAGACCACTCGGCCAACCCTC 1 chrXIV:567948-568377 ( 4) GAATCATACCACTAGACCACACGCC 1 chrXII:92367-92779 ( 26) GAATCATACCACTAGACCACACGCC 1 chrX:390902-391002 ( 36) CGCTCTTCCTACTGAGCTACTGAAG 1 chrX:422776-422876 ( 34) CGCTCTTCCTACTGAGCTACTGAAG 1 chrIII:142597-142929 ( 33) GGATTTTACCACTAAACCACTTGCG 1 chrXVI:860210-860554 ( 48) GGATTTTACCACTAAACCACTTGCG 1 chrIV:83416-83714 ( 34) GGATTTTACCACTAAACCACTTGCG 1 chrVI:162068-162379 ( 56) GGATTTTACCACTAAACCACTTGCG 1 chrXV:980517-980929 ( 11) GAATCATTCCACTAGACCACACGCC 1 chrIII:123440-123770 ( 68) GAATCATACCTCTAGACCACACGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 41800 bayes= 11.5027 E= 1.6e-161 -412 140 135 -1245 -212 84 164 -1245 -112 218 -1245 -1245 -180 5 -23 83 -1245 105 -182 83 40 -1245 -1245 92 97 -140 -40 -80 46 155 -1245 -412 -1245 240 -1245 -1245 -12 124 30 -312 155 -1245 -140 -412 -1245 218 -1245 -112 -1245 -1245 -1245 169 -12 30 99 -154 -42 -23 168 -1245 -42 -1245 202 -1245 -1245 240 -1245 -1245 -1245 215 -1245 -95 169 -1245 -1245 -1245 52 112 -1245 -112 40 -40 77 -131 5 60 -8 -54 46 -108 92 -131 5 84 77 -412 -212 140 99 -254 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 56 E= 1.6e-161 0.017857 0.500000 0.482143 0.000000 0.071429 0.339286 0.589286 0.000000 0.142857 0.857143 0.000000 0.000000 0.089286 0.196429 0.160714 0.553571 0.000000 0.392857 0.053571 0.553571 0.410714 0.000000 0.000000 0.589286 0.607143 0.071429 0.142857 0.178571 0.428571 0.553571 0.000000 0.017857 0.000000 1.000000 0.000000 0.000000 0.285714 0.446429 0.232143 0.035714 0.910714 0.000000 0.071429 0.017857 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 1.000000 0.285714 0.232143 0.375000 0.107143 0.232143 0.160714 0.607143 0.000000 0.232143 0.000000 0.767857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.839286 0.000000 0.160714 1.000000 0.000000 0.000000 0.000000 0.446429 0.410714 0.000000 0.142857 0.410714 0.142857 0.321429 0.125000 0.321429 0.285714 0.178571 0.214286 0.428571 0.089286 0.357143 0.125000 0.321429 0.339286 0.321429 0.017857 0.071429 0.500000 0.375000 0.053571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SSCTYWAMCVACTVGGCCAMRNRVS MEME-2 regular expression -------------------------------------------------------------------------------- [CG][GC]CT[TC][TA]A[CA]C[CAG]ACT[GAC][GA][GA]CCA[AC][AG][ACT][AG][CAG][CG] -------------------------------------------------------------------------------- Time 572.28 secs. ******************************************************************************** ******************************************************************************** MOTIF TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 width = 29 sites = 21 llr = 450 E-value = 2.1e-053 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a:22:83:::::a:1a:3:35::::2:: pos.-specific C 2:::212:2::43::4:71652734:227 probability G ::a:42:7:8a:::4:::411:27:2323 matrix T 8::817::82:67:64:31313::6835: bits 2.4 * * 2.2 * * 1.9 * * 1.7 * * * * Relative 1.4 ** * ** * ** * * Entropy 1.2 ** **** * ** ** * (30.9 bits) 1.0 **** ********* ** * **** * 0.7 **** ********** ** * **** * 0.5 **** ************* * **** * 0.2 ************************** ** 0.0 ----------------------------- Multilevel TAGTGTAGTGGTTATCACGCCACGTTGTC consensus C ACGCA T CC GT TATATGCCGTGG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------------------- chrXII:797018-797367 + 43 2.34e-12 TCGTCCGATA TAGTGTAACGGCTATCACATCACGCTTTC ACCGTGGAGA chrVII:779470-779796 + 40 2.34e-12 CCCGGGCGGT TAGTGTAGTGGTTATCATCCCACCCTTCC AAGGTGGGGA chrXIV:96118-96462 - 37 2.34e-12 CATGGGCGGT TAGTGTAGTGGTTATCATCCCACCCTTCC AAGGTGGGGA chrXI:140948-141229 - 16 2.34e-12 TAATCCGATA TAGTGTAACGGCTATCACATCACGCTTTC ACCGTGGAGA chrIV:1017038-1017445 - 52 2.72e-12 CAATCCGATG TAGTGTAACGGCTATCACATCACGTTCTC ACCGTGGAGA chrV:207182-207610 + 18 3.64e-12 TTCGCCATCT TAGTATAGTGGTTAGTACACATCGTTGTG GCCGATGAAA chrXIII:362931-363267 + 22 3.64e-12 TTTGCCATCT TAGTATAGTGGTTAGTACACATCGTTGTG GCCGATGAAA chrVII:319596-319974 + 53 3.64e-12 TTAGCCATCT TAGTATAGTGGTTAGTACACATCGTTGTG GCCGATGAAA chrVII:110510-110861 - 26 3.64e-12 CCTGCCATCT TAGTATAGTGGTTAGTACACATCGTTGTG GCCGATGAAA chrVII:828528-828985 + 60 7.44e-11 GATTAGAAGT CAGACGCGTTGCCATTACGCCACGCGAGC TACTGTTTGT chrIV:568708-569135 - 11 7.44e-11 GATTAGAAGT CAGACGCGTTGCCATTACGCCACGCGAGC TACTATTTGT chrXI:162354-162727 + 40 7.44e-11 GATTAGAAGT CAGACGCGTTGCCATTACGCCACGCGAGC TAATATTTGT chrX:374369-374469 + 32 7.44e-11 GATTAGAAGT CAGACGCGTTGCCATTACGCCACGCGAGC TACTATTTGT chrVII:736136-736598 - 23 7.44e-11 GATTAGAAGT CAGACGCGTTGCCATTACGCCACGCGAGC TATTGAAATT chrIV:520776-521151 + 66 9.08e-11 TAGGGTCCTA TAGTGTAGTGGTTATCACTTTCGGTTTTG ATCCGG chrIV:645045-645426 - 4 9.08e-11 TACGGTCCTA TAGTGTAGTGGTTATCACTTTCGGTTTTG ATC chrIV:1075347-1075709 - 31 5.04e-10 ATTGTTCCAA TAGTGTAGCGGCTATCACGTTGCCTTCAC ACGGCAAAGG chrXII:818448-818783 + 51 2.24e-09 TATGCTCCTC TAGTGCAATGGTTAGCATGCATTCTTCCG GTGGCTGTGA chrX:541324-541424 + 51 2.73e-09 AAATCCGTGA TAGTTTAATGGTCAGAATGGGCGCTTGTC GCGTGCCAGA chrVII:544427-544828 - 36 2.73e-09 TCTTCCGTGA TAGTTTAATGGTCAGAATGGGCGCTTGTC GCGTGCCAGA chrIV:1256898-1257244 - 23 8.26e-09 TTAGCGAAAG TGGTTCAGTGGTTAGAATTCATGCTTCCC AAGCATGGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrXII:797018-797367 2.3e-12 42_[+3]_29 chrVII:779470-779796 2.3e-12 39_[+3]_32 chrXIV:96118-96462 2.3e-12 36_[-3]_35 chrXI:140948-141229 2.3e-12 15_[-3]_56 chrIV:1017038-1017445 2.7e-12 51_[-3]_20 chrV:207182-207610 3.6e-12 17_[+3]_54 chrXIII:362931-363267 3.6e-12 21_[+3]_50 chrVII:319596-319974 3.6e-12 52_[+3]_19 chrVII:110510-110861 3.6e-12 25_[-3]_46 chrVII:828528-828985 7.4e-11 59_[+3]_12 chrIV:568708-569135 7.4e-11 10_[-3]_61 chrXI:162354-162727 7.4e-11 39_[+3]_32 chrX:374369-374469 7.4e-11 31_[+3]_40 chrVII:736136-736598 7.4e-11 22_[-3]_49 chrIV:520776-521151 9.1e-11 65_[+3]_6 chrIV:645045-645426 9.1e-11 3_[-3]_68 chrIV:1075347-1075709 5e-10 30_[-3]_41 chrXII:818448-818783 2.2e-09 50_[+3]_21 chrX:541324-541424 2.7e-09 50_[+3]_21 chrVII:544427-544828 2.7e-09 35_[-3]_36 chrIV:1256898-1257244 8.3e-09 22_[-3]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TAGTSTAGTGGYYAKYACRCMWCSYTNTS width=29 seqs=21 chrXII:797018-797367 ( 43) TAGTGTAACGGCTATCACATCACGCTTTC 1 chrVII:779470-779796 ( 40) TAGTGTAGTGGTTATCATCCCACCCTTCC 1 chrXIV:96118-96462 ( 37) TAGTGTAGTGGTTATCATCCCACCCTTCC 1 chrXI:140948-141229 ( 16) TAGTGTAACGGCTATCACATCACGCTTTC 1 chrIV:1017038-1017445 ( 52) TAGTGTAACGGCTATCACATCACGTTCTC 1 chrV:207182-207610 ( 18) TAGTATAGTGGTTAGTACACATCGTTGTG 1 chrXIII:362931-363267 ( 22) TAGTATAGTGGTTAGTACACATCGTTGTG 1 chrVII:319596-319974 ( 53) TAGTATAGTGGTTAGTACACATCGTTGTG 1 chrVII:110510-110861 ( 26) TAGTATAGTGGTTAGTACACATCGTTGTG 1 chrVII:828528-828985 ( 60) CAGACGCGTTGCCATTACGCCACGCGAGC 1 chrIV:568708-569135 ( 11) CAGACGCGTTGCCATTACGCCACGCGAGC 1 chrXI:162354-162727 ( 40) CAGACGCGTTGCCATTACGCCACGCGAGC 1 chrX:374369-374469 ( 32) CAGACGCGTTGCCATTACGCCACGCGAGC 1 chrVII:736136-736598 ( 23) CAGACGCGTTGCCATTACGCCACGCGAGC 1 chrIV:520776-521151 ( 66) TAGTGTAGTGGTTATCACTTTCGGTTTTG 1 chrIV:645045-645426 ( 4) TAGTGTAGTGGTTATCACTTTCGGTTTTG 1 chrIV:1075347-1075709 ( 31) TAGTGTAGCGGCTATCACGTTGCCTTCAC 1 chrXII:818448-818783 ( 51) TAGTGCAATGGTTAGCATGCATTCTTCCG 1 chrX:541324-541424 ( 51) TAGTTTAATGGTCAGAATGGGCGCTTGTC 1 chrVII:544427-544828 ( 36) TAGTTTAATGGTCAGAATGGGCGCTTGTC 1 chrIV:1256898-1257244 ( 23) TGGTTCAGTGGTTAGAATTCATGCTTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 39600 bayes= 11.1851 E= 2.1e-053 -1104 33 -1104 129 161 -1104 -199 -1104 -1104 -1104 240 -1104 -38 -1104 -1104 129 -71 33 118 -112 -1104 -99 33 110 129 33 -1104 -1104 -12 -1104 192 -1104 -1104 1 -1104 138 -1104 -1104 201 -38 -1104 -1104 240 -1104 -1104 118 -1104 88 -1104 82 -1104 110 169 -1104 -1104 -1104 -1104 -1104 101 99 -112 118 -1104 46 169 -1104 -1104 -1104 -1104 192 -1104 -12 10 -99 118 -112 -1104 171 -99 -12 -12 133 -99 -112 61 1 -199 -12 -1104 192 33 -270 -1104 82 182 -1104 -1104 118 -1104 88 -1104 -1104 33 129 -38 1 60 -12 -270 1 33 75 -1104 182 82 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 21 E= 2.1e-053 0.000000 0.238095 0.000000 0.761905 0.952381 0.000000 0.047619 0.000000 0.000000 0.000000 1.000000 0.000000 0.238095 0.000000 0.000000 0.761905 0.190476 0.238095 0.428571 0.142857 0.000000 0.095238 0.238095 0.666667 0.761905 0.238095 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.190476 0.000000 0.809524 0.000000 0.000000 0.761905 0.238095 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.333333 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.380952 0.619048 0.142857 0.428571 0.000000 0.428571 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.333333 0.095238 0.428571 0.142857 0.000000 0.619048 0.095238 0.285714 0.285714 0.476190 0.095238 0.142857 0.476190 0.190476 0.047619 0.285714 0.000000 0.714286 0.238095 0.047619 0.000000 0.333333 0.666667 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.238095 0.761905 0.238095 0.190476 0.285714 0.285714 0.047619 0.190476 0.238095 0.523810 0.000000 0.666667 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGTSTAGTGGYYAKYACRCMWCSYTNTS MEME-3 regular expression -------------------------------------------------------------------------------- [TC]AG[TA][GC][TG][AC][GA]T[GT]G[TC][TC]A[TG][CT]A[CT][GA][CT][CA][AT][CG][GC][TC][TG][GTA][TG][CG] -------------------------------------------------------------------------------- Time 843.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:434013-434511 3.77e-05 61_[-1(4.66e-09)]_18 chrVII:148443-148769 5.05e-01 100 chrXII:951474-951687 6.49e-01 100 chrV:303061-303380 7.11e-01 100 chrX:121621-121721 1.00e+00 100 chrXII:728129-728630 9.91e-01 100 chrVI:157815-158170 8.39e-05 39_[+2(1.66e-08)]_36 chrVII:736136-736598 3.60e-15 22_[-3(7.44e-11)]_12_[+1(6.27e-11)]_\ 16 chrIV:117861-118213 6.10e-01 100 chrX:76187-76287 9.98e-01 100 chrVIII:34374-34887 9.70e-02 100 chrXVI:789699-789832 3.45e-02 100 chrXIV:642302-642667 8.99e-01 100 chrXII:673760-674441 8.50e-01 100 chrIV:364480-365004 4.69e-01 100 chrXIV:560551-560935 3.87e-11 9_[-1(4.66e-09)]_16_[+2(1.67e-09)]_\ 29 chrVII:986901-987123 5.09e-01 100 chrXVI:338732-339101 4.43e-02 100 chrXIII:123503-124027 7.54e-01 100 chrX:73598-73698 5.91e-01 100 chrV:386146-386975 8.24e-01 100 chrXII:962892-963217 2.24e-05 25_[+2(1.82e-08)]_50 chrVIII:222502-222980 5.82e-01 100 chrX:448721-448821 1.15e-01 100 chrXIV:302871-303657 4.90e-01 100 chrXI:140948-141229 4.04e-08 15_[-3(2.34e-12)]_56 chrXV:868672-869196 7.59e-01 100 chrXII:242481-242756 6.34e-01 100 chrXV:1027926-1028778 1.49e-01 100 chrXV:424396-424920 1.28e-01 100 chrII:373611-374135 5.08e-01 100 chrVII:561461-561903 1.37e-01 100 chrXVI:516159-516290 2.69e-01 100 chrXII:809195-809641 5.38e-01 100 chrIV:976156-976741 6.98e-01 100 chrXV:305032-305556 3.16e-01 100 chrII:86482-86910 1.44e-01 100 chrV:139479-140488 9.58e-01 100 chrXVI:718470-719419 4.21e-01 100 chrXIII:23780-25983 3.35e-01 100 chrXVI:74983-75250 8.95e-01 100 chrXIV:576938-577275 3.20e-01 100 chrXII:86868-87180 9.36e-02 100 chrII:606449-606775 9.88e-01 100 chrVIII:122323-122461 7.38e-01 100 chrXII:723258-723405 5.71e-01 100 chrIV:117761-117911 8.06e-01 100 chrXIII:753618-753769 6.74e-01 100 chrXII:1051994-1052262 4.46e-15 2_[-1(4.47e-10)]_17_[+2(1.30e-11)]_\ 35 chrXI:68525-69049 5.40e-01 100 chrVII:534026-534275 7.67e-01 100 chrXIV:102553-102893 4.81e-05 43_[-2(1.39e-08)]_32 chrXI:142595-143119 1.95e-01 100 chrXIII:753206-753431 3.17e-01 100 chrXV:505184-505456 5.86e-01 100 chrXV:384612-385136 9.71e-01 100 chrIV:356691-357394 4.74e-01 100 chrXV:980517-980929 7.28e-06 10_[-2(2.55e-07)]_65 chrIV:538925-539206 3.37e-02 100 chrIV:1233654-1234140 1.62e-01 100 chrXV:1004054-1004491 3.45e-01 100 chrVIII:386411-386723 9.78e-01 100 chrV:306567-306849 2.48e-01 100 chrXII:374174-374605 3.43e-10 16_[-2(1.82e-08)]_16_[+1(1.15e-07)]_\ 22 chrX:265461-265561 3.50e-02 100 chrXII:47429-48032 9.44e-01 100 chrXV:506458-506644 1.75e-01 100 chrX:602775-602875 1.71e-02 100 chrXIII:123109-123415 8.11e-01 100 chrVIII:554170-554374 9.79e-01 100 chrXIV:426875-427123 7.77e-01 100 chrVIII:75609-75964 2.94e-01 100 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chrXII:930813-931184 7.63e-01 100 chrXVI:435723-436139 4.04e-03 21_[-1(4.10e-05)]_58 chrXV:671066-671419 1.67e-01 100 chrVIII:160474-160998 7.37e-01 100 chrII:414030-414294 9.72e-01 100 chrXVI:576074-576408 9.56e-02 100 chrXV:978701-979225 1.56e-01 100 chrXII:510153-510677 2.81e-02 49_[+1(7.47e-05)]_30 chrXVI:645282-645876 7.37e-01 100 chrIV:1434477-1435001 4.75e-01 100 chrXII:263092-263496 7.16e-01 100 chrXVI:817982-818117 7.06e-01 100 chrXII:5523-5787 6.69e-01 100 chrVII:107666-108190 5.63e-01 100 chrIV:340386-340599 8.99e-01 100 chrVII:255145-255509 9.23e-01 100 chrIV:1017038-1017445 1.26e-14 25_[-1(2.97e-10)]_5_[-3(2.72e-12)]_\ 20 chrIV:1354956-1355201 5.34e-01 100 chrXI:284287-284738 9.29e-01 100 chrXII:708275-708493 9.94e-01 100 chrXI:617818-618342 8.07e-01 100 chrV:322032-322911 6.90e-01 100 chrVII:771979-772277 3.92e-01 100 chrXIV:414254-414593 1.34e-01 100 chrXVI:282272-282727 7.96e-01 100 chrI:142158-143530 2.95e-01 100 chrXIII:631907-632332 9.59e-01 100 chrXV:79685-80209 8.37e-01 100 chrV:124046-124570 3.22e-01 100 chrVII:478118-478642 4.15e-01 100 chrXII:1029782-1030096 9.54e-01 100 chrXIII:661707-662084 6.75e-01 100 chrXI:384849-385373 1.06e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kali.stanford.edu ********************************************************************************