******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) 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= sequences.fa CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1 1.0000 151 2 1.0000 151 3 1.0000 151 4 1.0000 151 5 1.0000 151 6 1.0000 151 7 1.0000 151 8 1.0000 151 9 1.0000 151 10 1.0000 151 11 1.0000 151 12 1.0000 151 13 1.0000 151 14 1.0000 151 15 1.0000 151 16 1.0000 151 17 1.0000 151 18 1.0000 151 19 1.0000 151 20 1.0000 151 21 1.0000 151 22 1.0000 151 23 1.0000 151 24 1.0000 151 25 1.0000 151 26 1.0000 151 27 1.0000 151 28 1.0000 151 29 1.0000 151 30 1.0000 151 31 1.0000 151 32 1.0000 151 33 1.0000 151 34 1.0000 151 35 1.0000 151 36 1.0000 151 37 1.0000 151 38 1.0000 151 39 1.0000 151 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme sequences.fa -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 6 -maxw 50 -objfun classic -revcomp -markov_order 0 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 39 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 5889 N= 39 sample: seed= 0 hsfrac= 0 searchsize= 5889 norand= no csites= 1000 Letter frequencies in dataset: A 0.337 C 0.163 G 0.163 T 0.337 Background letter frequencies (from file dataset with add-one prior applied): A 0.337 C 0.163 G 0.163 T 0.337 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 width = 40 sites = 16 llr = 274 E-value = 4.6e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 663611233866866135334239711314:25:24:111 pos.-specific C 1:1:11141111:1:231:31:4:131:3113121::452 probability G 3:13:28:111:1::52:64173:112741842811a3:6 matrix T :46287:35123134234114111156:24123165:342 bits 2.6 * 2.4 * 2.1 * 1.8 * Relative 1.6 * * * Entropy 1.3 * * * * * * (24.7 bits) 1.0 * * * * * * * * 0.8 * * * * * * * * * * * ** 0.5 ** ***** * ***** * * ** ** * * **** 0.3 ******** ******* *** ******** ** ******* 0.0 ---------------------------------------- Multilevel AATATTGCTAAAAAAGCAGGTGCAATTGGAGGAGTTGCCG consensus GTAG TA T TT ATAAA A C ACT CT A TT sequence A T C G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------------------------------- 15 + 27 3.24e-14 TTTTTTAATT AATATTGATAAAAAAGGAGGGGCAATGGTTGGAGAAGTTG TTTTAGTCAA 24 - 85 2.41e-10 ACTATTTCCA CAAGCTGCAAGTAATGATACTGCAATTAGTGCACTTGCTG TAAGTCCAAT 9 + 78 5.12e-10 TGGTTTAAAA AATTTAGCGAAAATTGACGGAGCAGCTGCTGAAGTTGTTT TTGATTCACT 39 - 85 7.02e-10 AATCAATCCC AACATTGCAATTAATCCAACTAAAAGCGCTGGAGTAGTTG CGACTGATAC 28 + 51 7.02e-10 AGGTGAGCAA ATGATTATTACAATAGTTGGAGGAACAGGACTAGTTGGCC AAGGTATTTT 3 + 48 7.78e-10 AGGAGAAATA ATTATGGCAGATAAAGTTATTGCACTTGCATGTGCAGCCG GTATGTCAAC 23 + 72 1.06e-09 AGAAAATTAT GATGTTGTTGTCATTGGAGGAGGACATGCAGGGGTTGAAG CTTCACTAGC 1 + 48 2.12e-09 AGTATCTAAA GTTATGCCTAAAGAACCAGATTTAACCGGAGCAGAGGTTG TCAATATCTG 29 + 8 3.13e-09 TTTCCGA GAATTTGATAAAATAGATGATGTAATTGAAGAGGATGGTT AATATGAAAA 33 - 97 3.78e-09 ACGAACATAT AATATTGCTAGTAATATAAGTAAATCTAGGGCTGTTGCCC AGTAGATAAC 16 + 105 1.47e-08 AAAACCAGAA AATGTTGATCAAAAATCAGCTTATATTATTGGGGCAGGCC TTGCAGG 14 + 60 4.74e-08 TATGAAAAAA ATAATCACTAAAGATTACGCCACAATGAGTGAACTTGCTG CAGCGATTGT 5 + 78 4.74e-08 ACTACTTCTT CTTTTTGTGTTAAATATAGGAGGAAGTGGCGTACTAGCCA ATGATACTCA 37 - 58 7.62e-08 AAGTATAATG GTTGATGTCAACAAACCTAAAGAAATAAGAGTCGTTGTCT TTTTCATAAA 12 + 111 1.40e-07 GATAGCACTA ATAAATGTAAAAACATGTGAAGCATATGAACCTGGAGGCG T 19 + 60 3.80e-07 GATGAACAAG AAGATGAAAAAATTAGCATTGGGAATGGTCGGTTTGGCCG CAGTAGCAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15 3.2e-14 26_[+1]_85 24 2.4e-10 84_[-1]_27 9 5.1e-10 77_[+1]_34 39 7e-10 84_[-1]_27 28 7e-10 50_[+1]_61 3 7.8e-10 47_[+1]_64 23 1.1e-09 71_[+1]_40 1 2.1e-09 47_[+1]_64 29 3.1e-09 7_[+1]_104 33 3.8e-09 96_[-1]_15 16 1.5e-08 104_[+1]_7 14 4.7e-08 59_[+1]_52 5 4.7e-08 77_[+1]_34 37 7.6e-08 57_[-1]_54 12 1.4e-07 110_[+1]_1 19 3.8e-07 59_[+1]_52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG width=40 seqs=16 15 ( 27) AATATTGATAAAAAAGGAGGGGCAATGGTTGGAGAAGTTG 1 24 ( 85) CAAGCTGCAAGTAATGATACTGCAATTAGTGCACTTGCTG 1 9 ( 78) AATTTAGCGAAAATTGACGGAGCAGCTGCTGAAGTTGTTT 1 39 ( 85) AACATTGCAATTAATCCAACTAAAAGCGCTGGAGTAGTTG 1 28 ( 51) ATGATTATTACAATAGTTGGAGGAACAGGACTAGTTGGCC 1 3 ( 48) ATTATGGCAGATAAAGTTATTGCACTTGCATGTGCAGCCG 1 23 ( 72) GATGTTGTTGTCATTGGAGGAGGACATGCAGGGGTTGAAG 1 1 ( 48) GTTATGCCTAAAGAACCAGATTTAACCGGAGCAGAGGTTG 1 29 ( 8) GAATTTGATAAAATAGATGATGTAATTGAAGAGGATGGTT 1 33 ( 97) AATATTGCTAGTAATATAAGTAAATCTAGGGCTGTTGCCC 1 16 ( 105) AATGTTGATCAAAAATCAGCTTATATTATTGGGGCAGGCC 1 14 ( 60) ATAATCACTAAAGATTACGCCACAATGAGTGAACTTGCTG 1 5 ( 78) CTTTTTGTGTTAAATATAGGAGGAAGTGGCGTACTAGCCA 1 37 ( 58) GTTGATGTCAACAAACCTAAAGAAATAAGAGTCGTTGTCT 1 12 ( 111) ATAAATGTAAAAACATGTGAAGCATATGAACCTGGAGGCG 1 19 ( 60) AAGATGAAAAAATTAGCATTGGGAATGGTCGGTTTGGCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 40 n= 4368 bayes= 8.82655 E= 4.6e-006 89 -38 61 -1064 74 -1064 -1064 38 -43 -138 -38 74 74 -1064 61 -84 -143 -138 -1064 127 -243 -138 20 103 -84 -138 220 -1064 -43 142 -1064 -11 -11 -138 -38 57 115 -138 -38 -243 89 -138 -38 -84 89 -38 -1064 -43 127 -1064 -38 -243 89 -138 -1064 -11 74 -1064 -1064 38 -143 20 161 -84 -43 94 20 -43 57 -38 -1064 15 -11 -1064 194 -243 -43 61 120 -143 15 -138 -38 38 -84 -1064 207 -143 -43 120 61 -143 148 -1064 -1064 -243 103 -38 -138 -143 -143 61 -38 57 -143 -38 20 74 -11 -1064 207 -1064 -143 61 142 -84 38 -38 -138 15 -1064 -38 232 -243 -84 61 120 -84 57 -138 20 -43 -1064 20 220 -243 -84 -38 -138 89 15 -1064 -38 57 -1064 -1064 261 -1064 -243 120 61 -11 -243 161 -1064 38 -243 20 178 -84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 40 nsites= 16 E= 4.6e-006 0.625000 0.125000 0.250000 0.000000 0.562500 0.000000 0.000000 0.437500 0.250000 0.062500 0.125000 0.562500 0.562500 0.000000 0.250000 0.187500 0.125000 0.062500 0.000000 0.812500 0.062500 0.062500 0.187500 0.687500 0.187500 0.062500 0.750000 0.000000 0.250000 0.437500 0.000000 0.312500 0.312500 0.062500 0.125000 0.500000 0.750000 0.062500 0.125000 0.062500 0.625000 0.062500 0.125000 0.187500 0.625000 0.125000 0.000000 0.250000 0.812500 0.000000 0.125000 0.062500 0.625000 0.062500 0.000000 0.312500 0.562500 0.000000 0.000000 0.437500 0.125000 0.187500 0.500000 0.187500 0.250000 0.312500 0.187500 0.250000 0.500000 0.125000 0.000000 0.375000 0.312500 0.000000 0.625000 0.062500 0.250000 0.250000 0.375000 0.125000 0.375000 0.062500 0.125000 0.437500 0.187500 0.000000 0.687500 0.125000 0.250000 0.375000 0.250000 0.125000 0.937500 0.000000 0.000000 0.062500 0.687500 0.125000 0.062500 0.125000 0.125000 0.250000 0.125000 0.500000 0.125000 0.125000 0.187500 0.562500 0.312500 0.000000 0.687500 0.000000 0.125000 0.250000 0.437500 0.187500 0.437500 0.125000 0.062500 0.375000 0.000000 0.125000 0.812500 0.062500 0.187500 0.250000 0.375000 0.187500 0.500000 0.062500 0.187500 0.250000 0.000000 0.187500 0.750000 0.062500 0.187500 0.125000 0.062500 0.625000 0.375000 0.000000 0.125000 0.500000 0.000000 0.000000 1.000000 0.000000 0.062500 0.375000 0.250000 0.312500 0.062500 0.500000 0.000000 0.437500 0.062500 0.187500 0.562500 0.187500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTATTGHWAAAAWWGNWRVWGVAATTGSWGNWGTWGBYG MEME-1 regular expression -------------------------------------------------------------------------------- [AG][AT][TA][AG]TTG[CTA][TA]AA[AT]A[AT][AT]G[CAT][AT][GA][GAC][TA]G[CAG]AA[TC]T[GA][GC][AT]G[GC][AT]GT[TA]G[CTG][CT]G -------------------------------------------------------------------------------- Time 5.81 secs. ******************************************************************************** ******************************************************************************** MOTIF RAAAAAGCAMTTSA MEME-2 width = 14 sites = 18 llr = 184 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAAAAGCAMTTSA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 488779:28411:6 pos.-specific C ::2131:6131133 probability G 61:2::a2:21:71 matrix T :1::::::1:78:: bits 2.6 * 2.4 * 2.1 * 1.8 * Relative 1.6 * * Entropy 1.3 ** * (14.7 bits) 1.0 * * **** * 0.8 ********* *** 0.5 ************** 0.3 ************** 0.0 -------------- Multilevel GAAAAAGCAATTGA consensus A GC A C CC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAAGCAMTTSA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------- 34 + 123 6.45e-09 AAAAGCGCAA GAAAAAGCACTTGA AACAACAGCA 1 + 135 9.57e-09 TTTACTCGTA GAAAAAGCACTTGC TTG 18 + 57 6.28e-07 ATTCATGGAA GAAAAAGAACTTGA AAGGCGCAAA 32 + 75 6.67e-07 AACAGTTTTG AACAAAGCACTTGC AGTTGCTTTC 36 + 105 1.61e-06 TGACCAATCG AAAGAAGCAATTCA TGAAGCAGTC 38 - 62 3.85e-06 TTTCTTAGTT GAAGAAGCTCTTCA AGATTCTTCA 10 - 17 8.05e-06 CGAAATTCAA AAAACCGCAATTCA CACACTCATC 27 + 87 1.06e-05 AGGAAAAATG GGAAAAGCAATCGG TGATAATTTT 9 + 57 1.17e-05 TAAAATGAAT AAAAAAGAAATTGG TTTAAAAAAT 7 + 87 1.27e-05 AGAGCAAGAT AAACCCGCAGTTGC TAAATTCTAT 28 + 28 1.66e-05 AGGATAAGAA ATAAAAGCAAGTGA GGTGAGCAAA 14 + 36 1.95e-05 AAGTAACAAG AAAAAAGGAGCTCC TATGAAAAAA 2 - 102 2.10e-05 TTCTTTACCA GAACCAGAAAGTGA GATACCGTAA 22 + 120 2.27e-05 AATTCAAGAA GTCGAAGGAGTTGA AGTTGCGCAT 11 + 135 2.27e-05 TCCTCTCACT GGCACAGGAATTCA ACA 33 + 13 3.52e-05 GTAAAATAAT GAAAAAGCTCATCC TCAATAGCTT 24 + 53 3.52e-05 TTTTTATAAT GAAAAAGACATCGA AGAAAGTCAT 3 + 123 4.84e-05 AAAAATGCAA AAAGCAGCAGCAGA TAACGGGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAAGCAMTTSA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34 6.5e-09 122_[+2]_15 1 9.6e-09 134_[+2]_3 18 6.3e-07 56_[+2]_81 32 6.7e-07 74_[+2]_63 36 1.6e-06 104_[+2]_33 38 3.8e-06 61_[-2]_76 10 8e-06 16_[-2]_121 27 1.1e-05 86_[+2]_51 9 1.2e-05 56_[+2]_81 7 1.3e-05 86_[+2]_51 28 1.7e-05 27_[+2]_110 14 2e-05 35_[+2]_102 2 2.1e-05 101_[-2]_36 22 2.3e-05 119_[+2]_18 11 2.3e-05 134_[+2]_3 33 3.5e-05 12_[+2]_125 24 3.5e-05 52_[+2]_85 3 4.8e-05 122_[+2]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAAGCAMTTSA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAAAAAGCAMTTSA width=14 seqs=18 34 ( 123) GAAAAAGCACTTGA 1 1 ( 135) GAAAAAGCACTTGC 1 18 ( 57) GAAAAAGAACTTGA 1 32 ( 75) AACAAAGCACTTGC 1 36 ( 105) AAAGAAGCAATTCA 1 38 ( 62) GAAGAAGCTCTTCA 1 10 ( 17) AAAACCGCAATTCA 1 27 ( 87) GGAAAAGCAATCGG 1 9 ( 57) AAAAAAGAAATTGG 1 7 ( 87) AAACCCGCAGTTGC 1 28 ( 28) ATAAAAGCAAGTGA 1 14 ( 36) AAAAAAGGAGCTCC 1 2 ( 102) GAACCAGAAAGTGA 1 22 ( 120) GTCGAAGGAGTTGA 1 11 ( 135) GGCACAGGAATTCA 1 33 ( 13) GAAAAAGCTCATCC 1 24 ( 53) GAAAAAGACATCGA 1 3 ( 123) AAAGCAGCAGCAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAAGCAMTTSA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 5382 bayes= 9.62657 E= 1.8e+002 40 -1081 177 -1081 121 -1081 -55 -160 131 3 -1081 -1081 98 -55 45 -1081 110 77 -1081 -1081 140 -55 -1081 -1081 -1081 -1081 261 -1081 -60 190 3 -1081 131 -155 -1081 -160 40 103 45 -1081 -260 -55 -55 110 -260 -55 -1081 131 -1081 103 203 -1081 86 77 -55 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAAGCAMTTSA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 18 E= 1.8e+002 0.444444 0.000000 0.555556 0.000000 0.777778 0.000000 0.111111 0.111111 0.833333 0.166667 0.000000 0.000000 0.666667 0.111111 0.222222 0.000000 0.722222 0.277778 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.222222 0.611111 0.166667 0.000000 0.833333 0.055556 0.000000 0.111111 0.444444 0.333333 0.222222 0.000000 0.055556 0.111111 0.111111 0.722222 0.055556 0.111111 0.000000 0.833333 0.000000 0.333333 0.666667 0.000000 0.611111 0.277778 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAAGCAMTTSA MEME-2 regular expression -------------------------------------------------------------------------------- [GA]AA[AG][AC]AG[CA]A[ACG]TT[GC][AC] -------------------------------------------------------------------------------- Time 10.70 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGRAA MEME-3 width = 7 sites = 16 llr = 139 E-value = 6.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGRAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::a:6a6 pos.-specific C ::::::3 probability G aa:a4:: matrix T ::::::1 bits 2.6 ** * 2.4 ** * 2.1 ** * 1.8 ** * Relative 1.6 **** * Entropy 1.3 **** * (12.5 bits) 1.0 ****** 0.8 ****** 0.5 ******* 0.3 ******* 0.0 ------- Multilevel GGAGAAA consensus G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGRAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- 27 + 40 2.70e-05 CAATCTTAGA GGAGGAA GACTATGGCA 10 + 40 2.70e-05 TTTGAATTTC GGAGGAA AATAATGGCA 5 + 11 2.70e-05 TCGAAATGGG GGAGGAA ACTCTCCTAT 39 + 38 9.59e-05 CTAGACTAGA GGAGAAA AATAAAATGA 38 + 40 9.59e-05 AGTTAATCAA GGAGAAA ATCGTTGAAG 34 + 37 9.59e-05 AAAAGATAGA GGAGAAA TAATTTCATG 31 - 111 9.59e-05 TCTCCCTTTT GGAGAAA ATAGAAACGT 22 + 38 9.59e-05 ATAAAAAAAC GGAGGAC TACATCATGG 12 + 39 9.59e-05 TGGTTACTGA GGAGAAA TTTTAATGAA 4 + 41 9.59e-05 ATCTAGTTGA GGAGAAA TTTATGATAT 3 + 39 9.59e-05 TTAAGAATAA GGAGAAA TAATTATGGC 2 + 37 9.59e-05 TAAAATATTT GGAGGAC ATAAATTATG 13 + 53 1.23e-04 GAAATAAAAT GGAGAAC AAGGACAGAC 8 + 40 1.23e-04 AAGAATTAAA GGAGAAC ACACATGGCA 20 + 39 1.50e-04 ATAAATAAAT GGAGGAT TTAACATGAA 7 + 39 2.06e-04 CCTCAAAATA GGAGAAT GTAAGATGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGRAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27 2.7e-05 39_[+3]_105 10 2.7e-05 39_[+3]_105 5 2.7e-05 10_[+3]_134 39 9.6e-05 37_[+3]_107 38 9.6e-05 39_[+3]_105 34 9.6e-05 36_[+3]_108 31 9.6e-05 110_[-3]_34 22 9.6e-05 37_[+3]_107 12 9.6e-05 38_[+3]_106 4 9.6e-05 40_[+3]_104 3 9.6e-05 38_[+3]_106 2 9.6e-05 36_[+3]_108 13 0.00012 52_[+3]_92 8 0.00012 39_[+3]_105 20 0.00015 38_[+3]_106 7 0.00021 38_[+3]_106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGRAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGRAA width=7 seqs=16 27 ( 40) GGAGGAA 1 10 ( 40) GGAGGAA 1 5 ( 11) GGAGGAA 1 39 ( 38) GGAGAAA 1 38 ( 40) GGAGAAA 1 34 ( 37) GGAGAAA 1 31 ( 111) GGAGAAA 1 22 ( 38) GGAGGAC 1 12 ( 39) GGAGAAA 1 4 ( 41) GGAGAAA 1 3 ( 39) GGAGAAA 1 2 ( 37) GGAGGAC 1 13 ( 53) GGAGAAC 1 8 ( 40) GGAGAAC 1 20 ( 39) GGAGGAT 1 7 ( 39) GGAGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGRAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 5655 bayes= 9.19983 E= 6.2e+002 -1064 -1064 261 -1064 -1064 -1064 261 -1064 157 -1064 -1064 -1064 -1064 -1064 261 -1064 89 -1064 120 -1064 157 -1064 -1064 -1064 89 61 -1064 -143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGRAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 16 E= 6.2e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.625000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.625000 0.250000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGRAA MEME-3 regular expression -------------------------------------------------------------------------------- GGAG[AG]A[AC] -------------------------------------------------------------------------------- Time 14.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 2.62e-10 47_[+1(2.12e-09)]_[-2(7.60e-05)]_33_\ [+2(9.57e-09)]_3 2 7.45e-03 36_[+3(9.59e-05)]_58_[-2(2.10e-05)]_\ 36 3 1.90e-08 38_[+3(9.59e-05)]_2_[+1(7.78e-10)]_\ 35_[+2(4.84e-05)]_15 4 6.83e-02 40_[+3(9.59e-05)]_72_[+3(2.70e-05)]_\ 25 5 3.51e-06 10_[+3(2.70e-05)]_60_[+1(4.74e-08)]_\ 34 6 2.16e-01 151 7 6.53e-03 86_[+2(1.27e-05)]_51 8 2.81e-01 151 9 7.14e-08 56_[+2(1.17e-05)]_7_[+1(5.12e-10)]_\ 34 10 7.89e-04 16_[-2(8.05e-06)]_9_[+3(2.70e-05)]_\ 105 11 6.27e-03 134_[+2(2.27e-05)]_3 12 7.29e-05 38_[+3(9.59e-05)]_65_[+1(1.40e-07)]_\ 1 13 1.53e-01 151 14 7.04e-06 35_[+2(1.95e-05)]_10_[+1(4.74e-08)]_\ 52 15 3.91e-11 26_[+1(3.24e-14)]_85 16 2.00e-05 104_[+1(1.47e-08)]_7 17 1.56e-01 151 18 1.36e-03 56_[+2(6.28e-07)]_81 19 4.40e-05 59_[+1(3.80e-07)]_52 20 5.41e-02 151 21 1.50e-01 151 22 1.86e-03 37_[+3(9.59e-05)]_75_[+2(2.27e-05)]_\ 18 23 3.24e-07 71_[+1(1.06e-09)]_40 24 6.85e-08 52_[+2(3.52e-05)]_18_[-1(2.41e-10)]_\ 27 25 8.85e-01 151 26 5.51e-01 151 27 4.71e-04 39_[+3(2.70e-05)]_40_[+2(1.06e-05)]_\ 51 28 2.03e-09 27_[+2(1.66e-05)]_9_[+1(7.02e-10)]_\ 61 29 3.50e-05 7_[+1(3.13e-09)]_104 30 5.63e-01 151 31 1.00e-01 110_[-3(9.59e-05)]_34 32 3.15e-04 74_[+2(6.67e-07)]_63 33 1.07e-06 12_[+2(3.52e-05)]_70_[-1(3.78e-09)]_\ 15 34 2.70e-06 36_[+3(9.59e-05)]_79_[+2(6.45e-09)]_\ 15 35 8.44e-01 151 36 1.49e-04 59_[+1(1.94e-05)]_5_[+2(1.61e-06)]_\ 33 37 7.42e-05 57_[-1(7.62e-08)]_54 38 1.24e-04 39_[+3(9.59e-05)]_15_[-2(3.85e-06)]_\ 76 39 2.30e-07 37_[+3(9.59e-05)]_40_[-1(7.02e-10)]_\ 27 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************