******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -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= Train.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Operon104 1.0000 150 Operon2107 1.0000 150 Operon2284 1.0000 150 Operon807 1.0000 150 Operon1350 1.0000 150 Operon516 1.0000 150 Operon1380 1.0000 150 Operon1443 1.0000 150 Operon975 1.0000 150 Operon2084 1.0000 150 Operon126 1.0000 150 Operon551 1.0000 150 Operon1930 1.0000 150 Operon48 1.0000 150 Operon1767 1.0000 150 Operon44 1.0000 150 Operon2163 1.0000 150 Operon910 1.0000 150 Operon1391 1.0000 150 Operon1589 1.0000 150 Operon2094 1.0000 150 Operon1895 1.0000 150 Operon1834 1.0000 150 Operon1921 1.0000 150 Operon652 1.0000 150 Operon734 1.0000 150 Operon1644 1.0000 150 Operon2162 1.0000 150 Operon411 1.0000 150 Operon934 1.0000 150 Operon1817 1.0000 150 Operon724 1.0000 150 Operon95 1.0000 150 Operon2080 1.0000 150 Operon1706 1.0000 150 Operon580 1.0000 150 Operon1510 1.0000 150 Operon2244 1.0000 150 Operon1970 1.0000 150 Operon539 1.0000 150 Operon35 1.0000 150 Operon481 1.0000 150 Operon707 1.0000 150 Operon665 1.0000 150 Operon1122 1.0000 150 Operon849 1.0000 150 Operon1931 1.0000 150 Operon962 1.0000 150 Operon1523 1.0000 150 Operon2061 1.0000 150 Operon881 1.0000 150 Operon842 1.0000 150 Operon210 1.0000 150 Operon1587 1.0000 150 Operon448 1.0000 150 Operon418 1.0000 150 Operon1934 1.0000 150 Operon2124 1.0000 150 Operon2255 1.0000 150 Operon1730 1.0000 150 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme Train.fasta -dna -nmotifs 3 -minw 6 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= 60 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= 9000 N= 60 sample: seed= 0 hsfrac= 0 searchsize= 9000 norand= no csites= 1000 Letter frequencies in dataset: A 0.318 C 0.17 G 0.22 T 0.292 Background letter frequencies (from file dataset with add-one prior applied): A 0.318 C 0.17 G 0.22 T 0.292 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGGTGGWACCRCGRGWYA MEME-1 width = 18 sites = 6 llr = 121 E-value = 2.1e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTGGWACCRCGRGWYA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:::::3a::3::3:728 pos.-specific C :::2::::8a:a::::32 probability G 8aa:aa::::7:a78::: matrix T :::8::7:2:::::235: bits 2.6 * * 2.3 ** ** * ** 2.0 ** ** * ** 1.8 ** ** ** ** Relative 1.5 *** ** *** ** * Entropy 1.3 ****** *** ** * * (29.1 bits) 1.0 ****** ******** * 0.8 **************** * 0.5 ****************** 0.3 ****************** 0.0 ------------------ Multilevel GGGTGGTACCGCGGGATA consensus A A A TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGGWACCRCGRGWYA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ Operon910 63 5.27e-11 TTTTCTAAAA GGGTGGTACCGCGAGATA AGCTTTCTCG Operon1706 1 6.06e-11 . GGGTGGTACCGCGGGAAA ACGAAAGTCT Operon2094 59 2.66e-10 TCGGGAACTT GGGTGGAACCACGGGTTA ATCACACACT Operon665 62 7.58e-10 GGAATAATCA GGGTGGTACCACGGTTCA TTCGTCCCTT Operon104 24 1.14e-09 CTGTTAATAA AGGTGGTACCGCGAGACC CTCGTCCTTT Operon1934 109 1.24e-09 TGTCCACAAA GGGCGGAATCGCGGGATA AAACATTTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGGWACCRCGRGWYA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon910 5.3e-11 62_[+1]_70 Operon1706 6.1e-11 [+1]_132 Operon2094 2.7e-10 58_[+1]_74 Operon665 7.6e-10 61_[+1]_71 Operon104 1.1e-09 23_[+1]_109 Operon1934 1.2e-09 108_[+1]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGGWACCRCGRGWYA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGTGGWACCRCGRGWYA width=18 seqs=6 Operon910 ( 63) GGGTGGTACCGCGAGATA 1 Operon1706 ( 1) GGGTGGTACCGCGGGAAA 1 Operon2094 ( 59) GGGTGGAACCACGGGTTA 1 Operon665 ( 62) GGGTGGTACCACGGTTCA 1 Operon104 ( 24) AGGTGGTACCGCGAGACC 1 Operon1934 ( 109) GGGCGGAATCGCGGGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGGWACCRCGRGWYA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 7980 bayes= 10.8239 E= 2.1e-007 -93 -923 192 -923 -923 -923 218 -923 -923 -923 218 -923 -923 -3 -923 151 -923 -923 218 -923 -923 -923 218 -923 7 -923 -923 119 165 -923 -923 -923 -923 229 -923 -81 -923 255 -923 -923 7 -923 160 -923 -923 255 -923 -923 -923 -923 218 -923 7 -923 160 -923 -923 -923 192 -81 107 -923 -923 19 -93 97 -923 78 139 -3 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGGWACCRCGRGWYA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 6 E= 2.1e-007 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.833333 0.166667 0.666667 0.000000 0.000000 0.333333 0.166667 0.333333 0.000000 0.500000 0.833333 0.166667 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGGWACCRCGRGWYA MEME-1 regular expression -------------------------------------------------------------------------------- GGGTGG[TA]ACC[GA]CG[GA]G[AT][TC]A -------------------------------------------------------------------------------- Time 4.31 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTYWTBWTWTTCW MEME-2 width = 15 sites = 31 llr = 276 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTYWTBWTWTTCW MEME-2 Description -------------------------------------------------------------------------------- Simplified A :2:::3::5:411:5 pos.-specific C 32:241141::118: probability G 21:::223:11::1: matrix T 55a865734959815 bits 2.6 2.3 2.0 1.8 Relative 1.5 * * Entropy 1.3 ** * * (12.8 bits) 1.0 *** * *** 0.8 *** * * **** 0.5 * *** ********* 0.3 *************** 0.0 --------------- Multilevel TTTTTTTCATTTTCT consensus CC CA TT A A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYWTBWTWTTCW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- Operon910 111 2.46e-07 GATGAGAGGG CTTTTTTTATTTTCT GAAAAAATGC Operon1934 12 6.49e-07 CACTGGCATT TTTTCTGCATTTTCT CGATGATACA Operon807 44 7.77e-07 GATACGGCCT TTTTTATGTTTTTCT AGAGCACCTT Operon551 75 1.52e-06 AAAACATAGA TTTTCGTTTTTTTCT GTTATAATGC Operon1730 18 2.45e-06 TCGGTTAGAT TATTCTTCCTATTCT TAAATGCCAT Operon418 13 4.65e-06 TTCGATTTTC TTTCCGTCATATTCA AGCGTCTGCG Operon707 63 8.68e-06 CCCCTCAATT TTTTCATCTTTCTCT ACTGCCAAGG Operon481 39 9.75e-06 GGCCGGAATG GCTCTTTTATTTTCA TTTTTCAATT Operon35 31 1.21e-05 GCCTATATTA TCTTTTTCTTAATCT GAATGGTGCA Operon126 95 1.21e-05 GCGGGCAAGT CATTTTGCCTATTCT GGTGTCACCA Operon1895 8 1.35e-05 ATATGCC GGTTTTTGTTTTTCA TTGACACTTT Operon1767 3 1.35e-05 AG CCTTTGGTATTTTCA GTTTACCCCC Operon104 65 1.35e-05 TAGGACGGGG GTTTTTTGTGTTTCT TAAAGGAGGT Operon2244 77 1.66e-05 AGTGCAAAAT TCTTTTGCATATCCT CTCCGTTTTT Operon2094 111 2.06e-05 GGACGGGTGT GTTTTTTTATATACA ACAATGAATA Operon842 56 2.28e-05 CGAGGTGCTG TCTTTTTTTTATTTA TCTGTTGACA Operon1644 20 2.53e-05 GTAACGATTC GCTTTTTGTTATACA ATTGGAGCAA Operon48 63 2.80e-05 TAATGGAGGG TTTTCTTGTGGTTCT AAGCATAAGA Operon1122 64 3.08e-05 TATCACAGCT TATTTCTGCTATTCA ATCCAGGAAT Operon881 86 3.69e-05 TTTTAGCAGG CATTCACCTTTTTCA TCAAAAGAGA Operon44 90 4.02e-05 CATGGCAAGG TGTTCAGGTTTTTCT CACGGAGAAC Operon1930 27 4.80e-05 AAGTCTTGTA CTTTGATTTTTTTCA AAATATAATG Operon580 27 6.25e-05 TCCTCTACAA CTTTTATGATGTCCA GAACCCTGTC Operon665 113 7.93e-05 GAATGAGCCT TTTTTATTATGTTTT AAGAAATGAG Operon1817 115 7.93e-05 TTCTTCAATG TATCTATCATACTCT TCGGATTAAA Operon934 99 1.25e-04 TAAACGGCTG CTTTCTTCATTATGT ATGAACTTAC Operon2107 41 1.25e-04 GTTAGACAAA TTTCTGTTCGATTCA ACAAGTTTTT Operon411 96 1.55e-04 CGGCGCGCCT TATTTCTTATATTTA TTGAAATTCG Operon1970 103 1.89e-04 GAGCCGCGGA GCTTCGCGATTTACT TTTAGAGCTA Operon975 100 1.89e-04 GAGGTTATTG TTGTCTTCATATTGA AATAAAGATT Operon448 103 2.93e-04 GACTGGCACA CTTCTTGCATTTATA ATGGTGAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYWTBWTWTTCW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon910 2.5e-07 110_[+2]_25 Operon1934 6.5e-07 11_[+2]_124 Operon807 7.8e-07 43_[+2]_92 Operon551 1.5e-06 74_[+2]_61 Operon1730 2.5e-06 17_[+2]_118 Operon418 4.6e-06 12_[+2]_123 Operon707 8.7e-06 62_[+2]_73 Operon481 9.7e-06 38_[+2]_97 Operon35 1.2e-05 30_[+2]_105 Operon126 1.2e-05 94_[+2]_41 Operon1895 1.3e-05 7_[+2]_128 Operon1767 1.3e-05 2_[+2]_133 Operon104 1.3e-05 64_[+2]_71 Operon2244 1.7e-05 76_[+2]_59 Operon2094 2.1e-05 110_[+2]_25 Operon842 2.3e-05 55_[+2]_80 Operon1644 2.5e-05 19_[+2]_116 Operon48 2.8e-05 62_[+2]_73 Operon1122 3.1e-05 63_[+2]_72 Operon881 3.7e-05 85_[+2]_50 Operon44 4e-05 89_[+2]_46 Operon1930 4.8e-05 26_[+2]_109 Operon580 6.3e-05 26_[+2]_109 Operon665 7.9e-05 112_[+2]_23 Operon1817 7.9e-05 114_[+2]_21 Operon934 0.00012 98_[+2]_37 Operon2107 0.00012 40_[+2]_95 Operon411 0.00015 95_[+2]_40 Operon1970 0.00019 102_[+2]_33 Operon975 0.00019 99_[+2]_36 Operon448 0.00029 102_[+2]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYWTBWTWTTCW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTYWTBWTWTTCW width=15 seqs=31 Operon910 ( 111) CTTTTTTTATTTTCT 1 Operon1934 ( 12) TTTTCTGCATTTTCT 1 Operon807 ( 44) TTTTTATGTTTTTCT 1 Operon551 ( 75) TTTTCGTTTTTTTCT 1 Operon1730 ( 18) TATTCTTCCTATTCT 1 Operon418 ( 13) TTTCCGTCATATTCA 1 Operon707 ( 63) TTTTCATCTTTCTCT 1 Operon481 ( 39) GCTCTTTTATTTTCA 1 Operon35 ( 31) TCTTTTTCTTAATCT 1 Operon126 ( 95) CATTTTGCCTATTCT 1 Operon1895 ( 8) GGTTTTTGTTTTTCA 1 Operon1767 ( 3) CCTTTGGTATTTTCA 1 Operon104 ( 65) GTTTTTTGTGTTTCT 1 Operon2244 ( 77) TCTTTTGCATATCCT 1 Operon2094 ( 111) GTTTTTTTATATACA 1 Operon842 ( 56) TCTTTTTTTTATTTA 1 Operon1644 ( 20) GCTTTTTGTTATACA 1 Operon48 ( 63) TTTTCTTGTGGTTCT 1 Operon1122 ( 64) TATTTCTGCTATTCA 1 Operon881 ( 86) CATTCACCTTTTTCA 1 Operon44 ( 90) TGTTCAGGTTTTTCT 1 Operon1930 ( 27) CTTTGATTTTTTTCA 1 Operon580 ( 27) CTTTTATGATGTCCA 1 Operon665 ( 113) TTTTTATTATGTTTT 1 Operon1817 ( 115) TATCTATCATACTCT 1 Operon934 ( 99) CTTTCTTCATTATGT 1 Operon2107 ( 41) TTTCTGTTCGATTCA 1 Operon411 ( 96) TATTTCTTATATTTA 1 Operon1970 ( 103) GCTTCGCGATTTACT 1 Operon975 ( 100) TTGTCTTCATATTGA 1 Operon448 ( 103) CTTCTTGCATTTATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYWTBWTWTTCW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8160 bayes= 8.74306 E= 1.5e-004 -1160 60 -19 91 -71 41 -177 82 -1160 -1160 -277 173 -1160 -8 -1160 152 -1160 106 -277 107 -30 -140 -45 82 -1160 -140 -19 135 -1160 118 40 14 61 -40 -1160 41 -1160 -1160 -119 163 40 -1160 -119 73 -230 -140 -1160 158 -130 -140 -1160 147 -1160 224 -177 -118 61 -1160 -1160 82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYWTBWTWTTCW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 31 E= 1.5e-004 0.000000 0.258065 0.193548 0.548387 0.193548 0.225806 0.064516 0.516129 0.000000 0.000000 0.032258 0.967742 0.000000 0.161290 0.000000 0.838710 0.000000 0.354839 0.032258 0.612903 0.258065 0.064516 0.161290 0.516129 0.000000 0.064516 0.193548 0.741935 0.000000 0.387097 0.290323 0.322581 0.483871 0.129032 0.000000 0.387097 0.000000 0.000000 0.096774 0.903226 0.419355 0.000000 0.096774 0.483871 0.064516 0.064516 0.000000 0.870968 0.129032 0.064516 0.000000 0.806452 0.000000 0.806452 0.064516 0.129032 0.483871 0.000000 0.000000 0.516129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYWTBWTWTTCW MEME-2 regular expression -------------------------------------------------------------------------------- [TC][TC]TT[TC][TA]T[CTG][AT]T[TA]TTC[TA] -------------------------------------------------------------------------------- Time 8.64 secs. ******************************************************************************** ******************************************************************************** MOTIF AAGGAGGR MEME-3 width = 8 sites = 60 llr = 348 E-value = 2.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAGGAGGR MEME-3 Description -------------------------------------------------------------------------------- Simplified A 771:7:33 pos.-specific C 1:::::11 probability G 11aa3a54 matrix T 22::::12 bits 2.6 2.3 * 2.0 * * 1.8 ** * Relative 1.5 ** * Entropy 1.3 ** * (8.4 bits) 1.0 ** * 0.8 **** 0.5 ****** 0.3 ******** 0.0 -------- Multilevel AAGGAGGG consensus G AA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGGAGGR MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- Operon2163 136 1.66e-05 TGCAGGACCA AAGGAGGG TCATCTT Operon44 137 1.66e-05 TGTAGGCGAA AAGGAGGG AAAATA Operon1930 136 1.66e-05 TTTATGTTTC AAGGAGGG GTTTGGG Operon2284 134 1.66e-05 ATGAAAAAGA AAGGAGGG AAATGACAA Operon104 137 5.20e-05 ATGAGTTAGA AAGGAGGA TATCAA Operon1706 135 7.40e-05 ATTCAATCAG AAGGAGGT TTTTACTT Operon95 137 1.15e-04 TATCGTTCTA AAGGGGGA TTCATT Operon2162 136 1.15e-04 TACAATAACA AAGGGGGA TGTTAGA Operon807 138 1.15e-04 TATTGCGGAG AAGGAGAG GAATC Operon48 55 1.30e-04 CTCCGGAGTA ATGGAGGG TTTTCTTGTG Operon448 136 2.01e-04 CCCTAAATAG AAGGAGGC GCACAAA Operon2061 135 2.01e-04 AATCTGGTCC TAGGAGGG TAAAAGCA Operon1931 134 2.01e-04 ACAATGAAGA AAGGGGAG TGAGCAAGA Operon580 138 2.01e-04 AAAACACTAT AAGGGGAG AAACT Operon724 134 2.01e-04 GAATTCTTTC AAGGGGAG TGACCGTAC Operon1443 132 2.01e-04 CCAATGCTTA AAGGGGAG GGTTCTTCTC Operon962 117 2.12e-04 GAATGCTATA ATGGGGGG AGATTTATAA Operon539 138 2.66e-04 TGAAAAAGTG AAGGAGTG GCACA Operon1644 133 2.66e-04 AAATATCCAT AAGGAGTG TTTAGGAGAA Operon2094 135 2.66e-04 AACAATGAAT AAGGAGTG TTCTAAAA Operon1921 138 3.52e-04 CACATTTGCA AAGGAGAA CAATA Operon1730 138 4.31e-04 GATTTATTGA AAGGAGAT ACCCA Operon1589 135 4.31e-04 ACAAGGCTTG AGGGAGGA ATGTGAAT Operon2084 134 4.31e-04 ATCACGTATG AGGGAGGA ACTCACGCA Operon1380 135 4.31e-04 TAAAGACGTA AGGGAGGA TACAATCA Operon1510 135 4.97e-04 CCTTTCAAAG ATGGAGGT CGAATGAA Operon1817 138 4.97e-04 CTTCGGATTA AAGGGGAA TTCAA Operon1391 134 4.97e-04 GATTGGAATA TAGGAGGA CATTAAACA Operon2244 136 5.56e-04 AAAATAATTG AGGGAGGT TCATACA Operon1587 135 6.93e-04 AAACATAATA TAGGAGGT GAGCTACA Operon35 139 6.93e-04 TGCTCATTGT GAGGAGGA CATT Operon411 136 6.93e-04 AGGAAACAGT AGGGAGAG GATACCA Operon652 139 6.93e-04 TAAAAACAGC AGGGAGAG CACT Operon2255 134 9.83e-04 GAGTATTTTG AGGGAGGC GTACAGAGA Operon2107 136 9.83e-04 TTCATAACAC GAGGGGGA CTACATA Operon481 139 1.09e-03 TTATAGAAAG TAGGGGAG AAAT Operon1350 133 1.09e-03 ACTAGGCTAA TAGGGGAG GATCACTGAA Operon2124 134 1.19e-03 TCTCATGGGA TTGGGGGG TCTGTAAAA Operon2080 134 1.19e-03 GAAAGCGTTG AAGGGGCT GTTCAGGCA Operon1834 136 1.19e-03 GATCGACAGA AAGGGGCT GAAGCAA Operon975 135 1.29e-03 AAGTATATTA GAGGGGAG TTGCTTTA Operon516 135 1.29e-03 CCGCTTCGAA AAGGAGCC ATTTAACA Operon842 138 1.38e-03 TTATCAACTA ATGGGGTG ATAAC Operon551 137 1.38e-03 AAAGATAAAT ATGGGGTG TTATTT Operon210 136 1.61e-03 GTAAAAAAGG AAAGAGGG CGAGGCA Operon881 137 1.69e-03 ACCCTTATAT CAGGAGGC TGAGAC Operon1523 137 1.98e-03 AAGCGCATTC TTGGAGGT GTAATA Operon1970 47 1.98e-03 CGTTGAACAG ATGGAGCA TGAAATGAAG Operon934 58 1.98e-03 TATGCTATAA TAGGGGAA TCCTACAGAA Operon734 138 1.98e-03 AAAACATGAA ATGGAGTA TAAAC Operon910 137 1.98e-03 AAAAAATGCA GTGGAGGA ATGAAA Operon418 136 2.33e-03 ATAAAAAGAA AAGGTGGT TTTTACA Operon1767 135 2.72e-03 TAATTTAACT TAGGAGTT GTTATGAA Operon707 134 2.90e-03 AGTAAAAAGA AAAGAGGA TTAAATATA Operon1122 134 3.10e-03 TAAAAAATGA CTGGAGGT TTGTTACGG Operon665 95 3.10e-03 CCCTTTTTTA CAGGGGAA GAATGAGCCT Operon1934 136 3.66e-03 AAAACATTTC GGGGAGTG AAGCGAG Operon1895 121 4.38e-03 GATACGCTTT GAAGAGGG AACCCTAAAT Operon849 139 5.53e-03 AAATGTTGGA AAGGTGCT GGAT Operon126 136 6.72e-03 AACAGACAGA AAGGAAGC GGCCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGGAGGR MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon2163 1.7e-05 135_[+3]_7 Operon44 1.7e-05 136_[+3]_6 Operon1930 1.7e-05 135_[+3]_7 Operon2284 1.7e-05 133_[+3]_9 Operon104 5.2e-05 136_[+3]_6 Operon1706 7.4e-05 134_[+3]_8 Operon95 0.00011 136_[+3]_6 Operon2162 0.00011 135_[+3]_7 Operon807 0.00011 137_[+3]_5 Operon48 0.00013 54_[+3]_88 Operon448 0.0002 135_[+3]_7 Operon2061 0.0002 134_[+3]_8 Operon1931 0.0002 133_[+3]_9 Operon580 0.0002 137_[+3]_5 Operon724 0.0002 133_[+3]_9 Operon1443 0.0002 131_[+3]_11 Operon962 0.00021 116_[+3]_26 Operon539 0.00027 137_[+3]_5 Operon1644 0.00027 132_[+3]_10 Operon2094 0.00027 134_[+3]_8 Operon1921 0.00035 137_[+3]_5 Operon1730 0.00043 137_[+3]_5 Operon1589 0.00043 134_[+3]_8 Operon2084 0.00043 133_[+3]_9 Operon1380 0.00043 134_[+3]_8 Operon1510 0.0005 134_[+3]_8 Operon1817 0.0005 137_[+3]_5 Operon1391 0.0005 133_[+3]_9 Operon2244 0.00056 135_[+3]_7 Operon1587 0.00069 134_[+3]_8 Operon35 0.00069 138_[+3]_4 Operon411 0.00069 135_[+3]_7 Operon652 0.00069 138_[+3]_4 Operon2255 0.00098 133_[+3]_9 Operon2107 0.00098 135_[+3]_7 Operon481 0.0011 138_[+3]_4 Operon1350 0.0011 132_[+3]_10 Operon2124 0.0012 133_[+3]_9 Operon2080 0.0012 133_[+3]_9 Operon1834 0.0012 135_[+3]_7 Operon975 0.0013 134_[+3]_8 Operon516 0.0013 134_[+3]_8 Operon842 0.0014 137_[+3]_5 Operon551 0.0014 136_[+3]_6 Operon210 0.0016 135_[+3]_7 Operon881 0.0017 136_[+3]_6 Operon1523 0.002 136_[+3]_6 Operon1970 0.002 46_[+3]_96 Operon934 0.002 57_[+3]_85 Operon734 0.002 137_[+3]_5 Operon910 0.002 136_[+3]_6 Operon418 0.0023 135_[+3]_7 Operon1767 0.0027 134_[+3]_8 Operon707 0.0029 133_[+3]_9 Operon1122 0.0031 133_[+3]_9 Operon665 0.0031 94_[+3]_48 Operon1934 0.0037 135_[+3]_7 Operon1895 0.0044 120_[+3]_22 Operon849 0.0055 138_[+3]_4 Operon126 0.0067 135_[+3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGGAGGR MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAGGAGGR width=8 seqs=60 Operon2163 ( 136) AAGGAGGG 1 Operon44 ( 137) AAGGAGGG 1 Operon1930 ( 136) AAGGAGGG 1 Operon2284 ( 134) AAGGAGGG 1 Operon104 ( 137) AAGGAGGA 1 Operon1706 ( 135) AAGGAGGT 1 Operon95 ( 137) AAGGGGGA 1 Operon2162 ( 136) AAGGGGGA 1 Operon807 ( 138) AAGGAGAG 1 Operon48 ( 55) ATGGAGGG 1 Operon448 ( 136) AAGGAGGC 1 Operon2061 ( 135) TAGGAGGG 1 Operon1931 ( 134) AAGGGGAG 1 Operon580 ( 138) AAGGGGAG 1 Operon724 ( 134) AAGGGGAG 1 Operon1443 ( 132) AAGGGGAG 1 Operon962 ( 117) ATGGGGGG 1 Operon539 ( 138) AAGGAGTG 1 Operon1644 ( 133) AAGGAGTG 1 Operon2094 ( 135) AAGGAGTG 1 Operon1921 ( 138) AAGGAGAA 1 Operon1730 ( 138) AAGGAGAT 1 Operon1589 ( 135) AGGGAGGA 1 Operon2084 ( 134) AGGGAGGA 1 Operon1380 ( 135) AGGGAGGA 1 Operon1510 ( 135) ATGGAGGT 1 Operon1817 ( 138) AAGGGGAA 1 Operon1391 ( 134) TAGGAGGA 1 Operon2244 ( 136) AGGGAGGT 1 Operon1587 ( 135) TAGGAGGT 1 Operon35 ( 139) GAGGAGGA 1 Operon411 ( 136) AGGGAGAG 1 Operon652 ( 139) AGGGAGAG 1 Operon2255 ( 134) AGGGAGGC 1 Operon2107 ( 136) GAGGGGGA 1 Operon481 ( 139) TAGGGGAG 1 Operon1350 ( 133) TAGGGGAG 1 Operon2124 ( 134) TTGGGGGG 1 Operon2080 ( 134) AAGGGGCT 1 Operon1834 ( 136) AAGGGGCT 1 Operon975 ( 135) GAGGGGAG 1 Operon516 ( 135) AAGGAGCC 1 Operon842 ( 138) ATGGGGTG 1 Operon551 ( 137) ATGGGGTG 1 Operon210 ( 136) AAAGAGGG 1 Operon881 ( 137) CAGGAGGC 1 Operon1523 ( 137) TTGGAGGT 1 Operon1970 ( 47) ATGGAGCA 1 Operon934 ( 58) TAGGGGAA 1 Operon734 ( 138) ATGGAGTA 1 Operon910 ( 137) GTGGAGGA 1 Operon418 ( 136) AAGGTGGT 1 Operon1767 ( 135) TAGGAGTT 1 Operon707 ( 134) AAAGAGGA 1 Operon1122 ( 134) CTGGAGGT 1 Operon665 ( 95) CAGGGGAA 1 Operon1934 ( 136) GGGGAGTG 1 Operon1895 ( 121) GAAGAGGG 1 Operon849 ( 139) AAGGTGCT 1 Operon126 ( 136) AAGGAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGGAGGR MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8580 bayes= 7.14975 E= 2.4e-003 114 -177 -114 -96 110 -1255 -72 -67 -267 -1255 211 -1255 -1255 -1255 218 -1255 103 -1255 52 -313 -425 -1255 216 -1255 -35 -103 128 -113 -17 -103 98 -54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGGAGGR MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 2.4e-003 0.700000 0.050000 0.100000 0.150000 0.683333 0.000000 0.133333 0.183333 0.050000 0.000000 0.950000 0.000000 0.000000 0.000000 1.000000 0.000000 0.650000 0.000000 0.316667 0.033333 0.016667 0.000000 0.983333 0.000000 0.250000 0.083333 0.533333 0.133333 0.283333 0.083333 0.433333 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGGAGGR MEME-3 regular expression -------------------------------------------------------------------------------- AAGG[AG]G[GA][GAT] -------------------------------------------------------------------------------- Time 12.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon104 8.01e-10 23_[+1(1.14e-09)]_23_[+2(1.35e-05)]_\ 2_[+3(7.40e-05)]_47_[+3(5.20e-05)]_6 Operon2107 4.60e-02 150 Operon2284 3.48e-04 133_[+3(1.66e-05)]_9 Operon807 3.29e-05 43_[+2(7.77e-07)]_92 Operon1350 1.99e-01 150 Operon516 5.20e-01 150 Operon1380 1.59e-01 150 Operon1443 2.15e-02 150 Operon975 7.59e-02 150 Operon2084 2.32e-01 150 Operon126 2.52e-02 94_[+2(1.21e-05)]_41 Operon551 2.27e-03 39_[+2(4.14e-06)]_20_[+2(1.52e-06)]_\ 61 Operon1930 1.10e-03 26_[+2(4.80e-05)]_94_[+3(1.66e-05)]_\ 7 Operon48 2.37e-03 62_[+2(2.80e-05)]_73 Operon1767 1.82e-02 2_[+2(1.35e-05)]_133 Operon44 7.31e-05 89_[+2(4.02e-05)]_32_[+3(1.66e-05)]_\ 6 Operon2163 3.63e-02 135_[+3(1.66e-05)]_7 Operon910 2.87e-11 62_[+1(5.27e-11)]_30_[+2(2.46e-07)]_\ 25 Operon1391 1.26e-01 150 Operon1589 2.86e-01 150 Operon2094 1.38e-09 58_[+1(2.66e-10)]_34_[+2(2.06e-05)]_\ 25 Operon1895 2.27e-02 7_[+2(1.35e-05)]_128 Operon1834 3.31e-01 150 Operon1921 3.97e-02 150 Operon652 3.93e-02 150 Operon734 5.84e-01 150 Operon1644 4.73e-03 19_[+2(2.53e-05)]_116 Operon2162 2.08e-02 150 Operon411 1.66e-02 150 Operon934 6.58e-02 150 Operon1817 1.08e-02 114_[+2(7.93e-05)]_21 Operon724 7.05e-02 150 Operon95 1.01e-01 150 Operon2080 5.14e-01 150 Operon1706 1.13e-08 [+1(6.06e-11)]_116_[+3(7.40e-05)]_8 Operon580 8.65e-03 26_[+2(6.25e-05)]_109 Operon1510 6.77e-02 150 Operon2244 7.50e-03 76_[+2(1.66e-05)]_59 Operon1970 3.65e-02 150 Operon539 6.28e-02 150 Operon35 6.85e-03 30_[+2(1.21e-05)]_105 Operon481 3.14e-03 38_[+2(9.75e-06)]_97 Operon707 8.86e-03 62_[+2(8.68e-06)]_73 Operon665 9.97e-08 61_[+1(7.58e-10)]_33_[+2(7.93e-05)]_\ 23 Operon1122 1.78e-02 63_[+2(3.08e-05)]_72 Operon849 6.19e-01 150 Operon1931 1.86e-01 150 Operon962 8.96e-02 150 Operon1523 3.03e-01 150 Operon2061 1.53e-01 150 Operon881 3.33e-02 85_[+2(3.69e-05)]_50 Operon842 1.79e-02 55_[+2(2.28e-05)]_80 Operon210 1.78e-01 150 Operon1587 3.23e-01 150 Operon448 2.28e-02 150 Operon418 3.17e-03 12_[+2(4.65e-06)]_123 Operon1934 2.15e-09 11_[+2(6.49e-07)]_82_[+1(1.24e-09)]_\ 24 Operon2124 2.80e-01 150 Operon2255 1.35e-01 150 Operon1730 3.32e-04 17_[+2(2.45e-06)]_118 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************