******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://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 ******************************************************************************** PRIMARY SEQUENCES= common/crp0.s CONTROL SEQUENCES= Primary sequences shuffled preserving 2-mers ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ce1cg 1.0000 105 ara 1.0000 105 bglr1 1.0000 105 crp 1.0000 105 cya 1.0000 105 deop2 1.0000 105 gale 1.0000 105 ilv 1.0000 105 lac 1.0000 105 male 1.0000 105 malk 1.0000 105 malt 1.0000 105 ompa 1.0000 105 tnaa 1.0000 105 uxu1 1.0000 105 pbr322 1.0000 105 trn9cat 1.0000 105 tdc 1.0000 105 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme common/crp0.s -oc results/meme28 -mod oops -dna -revcomp -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi model: mod= oops nmotifs= 2 evt= inf objective function: em= Selective mHG starts= log likelihood ratio (LLR) strands: + - width: minw= 12 maxw= 12 nsites: minsites= 18 maxsites= 18 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1890 N= 18 sample: seed= 0 hsfrac= 0.6 searchsize= 1890 norand= no csites= -1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from file dataset with add-one prior applied): A 0.304 C 0.196 G 0.196 T 0.304 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AHSGYAWWWAAT MEME-1 width = 12 sites = 18 llr = 103 p-value = 9.5e-002 E-value = 9.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AHSGYAWWWAAT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 931127654551 pos.-specific C :34253::122: probability G ::571:11:123 matrix T 14::3:446217 bits 2.4 2.1 1.9 1.6 Relative 1.4 * Entropy 1.2 * ** (8.3 bits) 0.9 * ** * 0.7 * ** * * 0.5 * ******* * 0.2 ************ 0.0 ------------ Multilevel ATGGCAAATAAT consensus ACCTCTTACCG sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHSGYAWWWAAT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ lac + 1 4.67e-06 . AACGCAATTAAT GTGAGTTAGC tdc + 31 9.21e-05 TTGATATTTA AAGGTATTTAAT TGTAATAACG deop2 + 20 1.06e-04 TTTGAACCAG ATCGCATTACAG TGATGCAAAC pbr322 - 45 1.23e-04 GGTATTTCAC ACCGCATATGGT GCACTCTCAG male + 6 1.86e-04 ACATT ACCGCCAATTCT GTAACAGAGA bglr1 + 5 1.86e-04 ACAA ATCCCAATAACT TAATTATTGG cya + 36 2.38e-04 ATCTTTCTTT ACGGTCAATCAG CAAGGTGTTA ara + 33 3.35e-04 GTCTATAATC ACGGCAGAAAAG TCCACATTGA malk + 55 5.01e-04 GAGGTCATGT AAGGAATTTCGT GATGTTGCTT tnaa + 45 7.27e-04 ATCTTTAAAA AAAGCATTTAAT ATTGCTCCCC crp + 16 7.95e-04 AGCGAAAGCT ATGCTAAAACAG TCAGGATGCT gale - 89 9.43e-04 GGCTT ATGGTATGAAAT AACCATAGCA trn9cat - 73 1.73e-03 ACGTCTCATT TTCGCCAAAAGT TGGCCCAGGG uxu1 + 32 1.99e-03 TGATGTGGTT AACCCAATTAGA ATTCGGGATT ilv - 74 2.93e-03 AGGGGAGACA ATGGAAAATTTT TCAGCAAAGG malt + 76 3.73e-03 CACATAAAAA AACGTCATCGCT TGCATTAGAA ompa - 36 3.95e-03 CGTCAGGCAT ATGAAAAAAAAG TCTTGTATAA ce1cg - 34 4.66e-03 CTTTCACACC ACGCGCTATTCT CGCCCGATGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHSGYAWWWAAT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- lac 4.7e-06 [+1]_93 tdc 9.2e-05 30_[+1]_63 deop2 0.00011 19_[+1]_74 pbr322 0.00012 44_[-1]_49 male 0.00019 5_[+1]_88 bglr1 0.00019 4_[+1]_89 cya 0.00024 35_[+1]_58 ara 0.00033 32_[+1]_61 malk 0.0005 54_[+1]_39 tnaa 0.00073 44_[+1]_49 crp 0.0008 15_[+1]_78 gale 0.00094 88_[-1]_5 trn9cat 0.0017 72_[-1]_21 uxu1 0.002 31_[+1]_62 ilv 0.0029 73_[-1]_20 malt 0.0037 75_[+1]_18 ompa 0.0039 35_[-1]_58 ce1cg 0.0047 33_[-1]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHSGYAWWWAAT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AHSGYAWWWAAT width=12 seqs=18 lac ( 1) AACGCAATTAAT 1 tdc ( 31) AAGGTATTTAAT 1 deop2 ( 20) ATCGCATTACAG 1 pbr322 ( 45) ACCGCATATGGT 1 male ( 6) ACCGCCAATTCT 1 bglr1 ( 5) ATCCCAATAACT 1 cya ( 36) ACGGTCAATCAG 1 ara ( 33) ACGGCAGAAAAG 1 malk ( 55) AAGGAATTTCGT 1 tnaa ( 45) AAAGCATTTAAT 1 crp ( 16) ATGCTAAAACAG 1 gale ( 89) ATGGTATGAAAT 1 trn9cat ( 73) TTCGCCAAAAGT 1 uxu1 ( 32) AACCCAATTAGA 1 ilv ( 74) ATGGAAAATTTT 1 malt ( 76) AACGTCATCGCT 1 ompa ( 36) ATGAAAAAAAAG 1 ce1cg ( 34) ACGCGCTATTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHSGYAWWWAAT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 6.53916 E= 9.5e-002 163 -1081 -1081 -245 13 50 -1081 35 -245 118 135 -1081 -245 18 188 -1081 -87 135 -182 -13 125 50 -1081 -1081 87 -1081 -182 35 72 -1081 -182 55 35 -182 -1081 87 72 18 -82 -87 72 18 18 -245 -245 -1081 50 113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHSGYAWWWAAT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 9.5e-002 0.944444 0.000000 0.000000 0.055556 0.333333 0.277778 0.000000 0.388889 0.055556 0.444444 0.500000 0.000000 0.055556 0.222222 0.722222 0.000000 0.166667 0.500000 0.055556 0.277778 0.722222 0.277778 0.000000 0.000000 0.555556 0.000000 0.055556 0.388889 0.500000 0.000000 0.055556 0.444444 0.388889 0.055556 0.000000 0.555556 0.500000 0.222222 0.111111 0.166667 0.500000 0.222222 0.222222 0.055556 0.055556 0.000000 0.277778 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AHSGYAWWWAAT MEME-1 regular expression -------------------------------------------------------------------------------- A[TAC][GC][GC][CT][AC][AT][AT][TA][AC][ACG][TG] -------------------------------------------------------------------------------- Time 0.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGADYDDDNTC MEME-2 width = 12 sites = 18 llr = 109 p-value = 9.7e-001 E-value = 9.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGADYDDDNTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :117413433:1 pos.-specific C 1::314111229 probability G 819:3233222: matrix T 18::23434371 bits 2.4 2.1 * 1.9 * 1.6 * * Relative 1.4 * * * Entropy 1.2 * * * (8.7 bits) 0.9 **** * 0.7 **** ** 0.5 **** * ** 0.2 ******** ** 0.0 ------------ Multilevel GTGAACTATATC consensus CGTAGAT sequence T GTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGADYDDDNTC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ bglr1 + 80 7.14e-06 GTTAATAACT GTGAGCATGGTC ATATTTTTAT lac + 13 2.30e-05 CGCAATTAAT GTGAGTTAGCTC ACTCATTAGG malk + 33 5.66e-05 CACGGCTTCT GTGAACTAAACC GAGGTCATGT tdc + 82 7.48e-05 AAGTTAATTT GTGAGTGGTCGC ACATATCCTG pbr322 - 59 7.48e-05 TTACGCATCT GTGCGGTATTTC ACACCGCATA deop2 + 64 8.59e-05 TTCCTTAATT GTGATGTGTATC GAAGTGTGTT ompa - 54 2.22e-04 ACTTACAAGT GTGAACTCCGTC AGGCATATGA tnaa - 77 2.44e-04 TTGTTTAAAT GTGAATCGAATC ACAATCGTTC ilv + 43 3.72e-04 AGTACAAAAC GTGATCAACCCC TCAATTTTCC malt - 47 4.06e-04 GTGTCTGAAT TTGCACTGTGTC ACAATTCCAA ce1cg + 65 6.24e-04 GACTGTTTTT TTGATCGTTTTC ACAAAAATGG ara - 53 1.04e-03 GTGTGACGCC GTGCAAATAATC AATGTGGACT cya - 56 1.32e-03 GGTCTAAAAC GTGATCAATTTA ACACCTTGCT gale + 28 1.43e-03 AAATTCTTGT GTAAACGATTCC ACTAATTTAT male + 46 1.54e-03 AGCGACGGTG GGGCGTAGGGGC AAGGAGGATG trn9cat + 88 2.19e-03 TGGCGAAAAT GAGACGTTGATC GGCACG crp + 57 3.58e-03 CATTGATGTA CTGCATGTATGC AAAGGACGTC uxu1 + 6 4.01e-03 CCCAT GAGAGTGAAATT GTTGTGATGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGADYDDDNTC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bglr1 7.1e-06 79_[+2]_14 lac 2.3e-05 12_[+2]_81 malk 5.7e-05 32_[+2]_61 tdc 7.5e-05 81_[+2]_12 pbr322 7.5e-05 58_[-2]_35 deop2 8.6e-05 63_[+2]_30 ompa 0.00022 53_[-2]_40 tnaa 0.00024 76_[-2]_17 ilv 0.00037 42_[+2]_51 malt 0.00041 46_[-2]_47 ce1cg 0.00062 64_[+2]_29 ara 0.001 52_[-2]_41 cya 0.0013 55_[-2]_38 gale 0.0014 27_[+2]_66 male 0.0015 45_[+2]_48 trn9cat 0.0022 87_[+2]_6 crp 0.0036 56_[+2]_37 uxu1 0.004 5_[+2]_88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGADYDDDNTC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGADYDDDNTC width=12 seqs=18 bglr1 ( 80) GTGAGCATGGTC 1 lac ( 13) GTGAGTTAGCTC 1 malk ( 33) GTGAACTAAACC 1 tdc ( 82) GTGAGTGGTCGC 1 pbr322 ( 59) GTGCGGTATTTC 1 deop2 ( 64) GTGATGTGTATC 1 ompa ( 54) GTGAACTCCGTC 1 tnaa ( 77) GTGAATCGAATC 1 ilv ( 43) GTGATCAACCCC 1 malt ( 47) TTGCACTGTGTC 1 ce1cg ( 65) TTGATCGTTTTC 1 ara ( 53) GTGCAAATAATC 1 cya ( 56) GTGATCAATTTA 1 gale ( 28) GTAAACGATTCC 1 male ( 46) GGGCGTAGGGGC 1 trn9cat ( 88) GAGACGTTGATC 1 crp ( 57) CTGCATGTATGC 1 uxu1 ( 6) GAGAGTGAAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGADYDDDNTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 6.53916 E= 9.7e-001 -1081 -182 209 -145 -145 -1081 -182 145 -245 -1081 227 -1081 125 50 -1081 -1081 35 -182 77 -45 -245 118 -23 13 -13 -182 50 35 35 -182 50 -13 -13 -82 18 35 13 -23 18 -13 -1081 -23 -23 113 -245 218 -1081 -245 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGADYDDDNTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 9.7e-001 0.000000 0.055556 0.833333 0.111111 0.111111 0.000000 0.055556 0.833333 0.055556 0.000000 0.944444 0.000000 0.722222 0.277778 0.000000 0.000000 0.388889 0.055556 0.333333 0.222222 0.055556 0.444444 0.166667 0.333333 0.277778 0.055556 0.277778 0.388889 0.388889 0.055556 0.277778 0.277778 0.277778 0.111111 0.222222 0.388889 0.333333 0.166667 0.222222 0.277778 0.000000 0.166667 0.166667 0.666667 0.055556 0.888889 0.000000 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGADYDDDNTC MEME-2 regular expression -------------------------------------------------------------------------------- GTG[AC][AGT][CT][TAG][AGT][TAG][ATG]TC -------------------------------------------------------------------------------- Time 0.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 2.42e-01 105 ara 4.94e-02 105 bglr1 5.06e-04 79_[+2(7.14e-06)]_14 crp 2.51e-01 105 cya 5.44e-02 105 deop2 2.87e-03 63_[+2(8.59e-05)]_30 gale 1.63e-01 105 ilv 1.31e-01 105 lac 1.36e-05 [+1(4.67e-06)]_2_[-2(5.54e-06)]_79 male 4.97e-02 105 malk 7.58e-03 32_[+2(5.66e-05)]_61 malt 1.59e-01 105 ompa 1.04e-01 105 tnaa 3.53e-02 105 uxu1 3.56e-01 105 pbr322 2.89e-03 58_[-2(7.48e-05)]_35 trn9cat 3.17e-01 105 tdc 2.24e-03 30_[+1(9.21e-05)]_39_[+2(7.48e-05)]_\ 12 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************