******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. 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.nbcr.net. ******************************************************************************** ******************************************************************************** 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= motifs/47/47.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 19501 1.0000 500 21871 1.0000 500 22476 1.0000 500 22535 1.0000 500 23025 1.0000 500 24262 1.0000 500 24410 1.0000 500 24423 1.0000 500 25949 1.0000 500 26046 1.0000 500 26063 1.0000 500 26137 1.0000 500 26221 1.0000 500 26250 1.0000 500 26367 1.0000 500 264201 1.0000 500 268372 1.0000 500 268651 1.0000 500 269086 1.0000 500 269235 1.0000 500 269779 1.0000 500 269961 1.0000 500 27167 1.0000 500 27292 1.0000 500 28049 1.0000 500 29007 1.0000 500 29217 1.0000 500 29825 1.0000 500 29955 1.0000 500 30154 1.0000 500 31084 1.0000 500 32675 1.0000 500 33241 1.0000 500 37032 1.0000 500 37628 1.0000 500 37809 1.0000 500 39282 1.0000 500 39424 1.0000 500 39550 1.0000 500 39735 1.0000 500 40312 1.0000 500 40329 1.0000 500 40387 1.0000 500 41319 1.0000 500 46 1.0000 500 802 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/47/47.seqs.fa -oc motifs/47 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 46 wnsites= 0.8 theta: prob= 1 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= 23000 N= 46 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.240 G 0.227 T 0.278 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.240 G 0.227 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 23 llr = 307 E-value = 3.4e-021 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 57252a::a9:143:9:56 pos.-specific C 3:7:1::::1312:::5:: probability G 11:33:aa::::27::1:: matrix T 11114:::::672:a:443 bits 2.1 * 1.9 *** 1.7 **** 1.5 ***** ** Relative 1.3 ***** ** Entropy 1.1 ***** ** (19.2 bits) 0.9 ** ***** * *** * 0.6 ** ******* **** * 0.4 *** ******* ****** 0.2 ******************* 0.0 ------------------- Multilevel AACATAGGAATTAGTACAA consensus C GG C CA TTT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 22535 55 7.20e-09 ATACGTCACT AACACAGGAATTTGTATAA AGTTGAGACG 23025 152 1.84e-08 AGCCGATGGT CATGTAGGAATTAGTATTA TTGCTACGAG 26367 325 2.68e-08 ATTTCTACAC CATAGAGGAACTGGTACAA CACCCGCCAT 26250 83 3.42e-08 CGAGAGTCAC GACAGAGGAACTCATACAT GGTCCATTGC 269961 376 3.83e-08 TAGGATCCCC AACAGAGGAATAAATATTT TTTACTAATG 30154 15 4.31e-08 CAGTAACGTT AACAAAAGAATTAGTATAA AAGTCTCAGT 802 384 4.84e-08 GTTGAATTTC AGCGAAGGAACTAGTACTT GTTATAAACA 27167 412 8.34e-08 GTCAATAATG AACGTAGGAACTGGTACCT TAGGTCGCCT 24262 220 1.54e-07 AGCGGTAATG CACATAGGAACATATACAT TTTTACGCGA 19501 327 1.54e-07 AAAAACTCCG CATAAAGGAATTCATATTA TTAATTCCAC 29217 240 2.27e-07 AACTTGCTCA CACAGAGGACATAGTACAA TCTACACGGA 27292 239 2.99e-07 ATTTTGGCTG AACGTAGGAATTGATTTTA AGACCACGCA 26063 326 3.27e-07 TGCGCTATTT ATAGTAGGAATTAGTACAG ACTCAAACGT 24423 184 3.27e-07 ACGCGAGGTT ACAAGAGGAATAAGTACAA ATTTGCTCCG 28049 226 3.58e-07 AGCGAATTTC AACAGAGGAATTCGTGGAT CGAGGCCAGG 269235 349 6.02e-07 CTAAATCTGC TACAAAGGAACTTGTAGTT ATCGTACGAG 26046 385 7.09e-07 GCGCGCAGTA ATATTAGGAATCAGTACAA AACCTTTGTA 37032 298 9.04e-07 CTTTACACGT TGCAGAGGAACCTGTACAA ATCCTGTACC 268372 45 9.77e-07 GGTGCTTTCA GACCAAGGAAGTAGTATAA TGAAGTAAAG 269779 330 1.33e-06 CTGTAGAATC AACGTAGGAATTCAAATGA AAAAGAGCTG 24410 280 1.33e-06 AAGCGGTAGC CACGTAGGAACCCTTACTT TTCTACGAGG 39735 154 2.06e-06 GCGGTAACAA ATATCAGGAATTAATATTA TTCTACATAC 41319 404 2.37e-06 GTAGAAGGTT GACGTTGGACTTGGTACTA CGTTCCCGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22535 7.2e-09 54_[+1]_427 23025 1.8e-08 151_[+1]_330 26367 2.7e-08 324_[+1]_157 26250 3.4e-08 82_[+1]_399 269961 3.8e-08 375_[+1]_106 30154 4.3e-08 14_[+1]_467 802 4.8e-08 383_[+1]_98 27167 8.3e-08 411_[+1]_70 24262 1.5e-07 219_[+1]_262 19501 1.5e-07 326_[+1]_155 29217 2.3e-07 239_[+1]_242 27292 3e-07 238_[+1]_243 26063 3.3e-07 325_[+1]_156 24423 3.3e-07 183_[+1]_298 28049 3.6e-07 225_[+1]_256 269235 6e-07 348_[+1]_133 26046 7.1e-07 384_[+1]_97 37032 9e-07 297_[+1]_184 268372 9.8e-07 44_[+1]_437 269779 1.3e-06 329_[+1]_152 24410 1.3e-06 279_[+1]_202 39735 2.1e-06 153_[+1]_328 41319 2.4e-06 403_[+1]_78 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=23 22535 ( 55) AACACAGGAATTTGTATAA 1 23025 ( 152) CATGTAGGAATTAGTATTA 1 26367 ( 325) CATAGAGGAACTGGTACAA 1 26250 ( 83) GACAGAGGAACTCATACAT 1 269961 ( 376) AACAGAGGAATAAATATTT 1 30154 ( 15) AACAAAAGAATTAGTATAA 1 802 ( 384) AGCGAAGGAACTAGTACTT 1 27167 ( 412) AACGTAGGAACTGGTACCT 1 24262 ( 220) CACATAGGAACATATACAT 1 19501 ( 327) CATAAAGGAATTCATATTA 1 29217 ( 240) CACAGAGGACATAGTACAA 1 27292 ( 239) AACGTAGGAATTGATTTTA 1 26063 ( 326) ATAGTAGGAATTAGTACAG 1 24423 ( 184) ACAAGAGGAATAAGTACAA 1 28049 ( 226) AACAGAGGAATTCGTGGAT 1 269235 ( 349) TACAAAGGAACTTGTAGTT 1 26046 ( 385) ATATTAGGAATCAGTACAA 1 37032 ( 298) TGCAGAGGAACCTGTACAA 1 268372 ( 45) GACCAAGGAAGTAGTATAA 1 269779 ( 330) AACGTAGGAATTCAAATGA 1 24410 ( 280) CACGTAGGAACCCTTACTT 1 39735 ( 154) ATATCAGGAATTAATATTA 1 41319 ( 404) GACGTTGGACTTGGTACTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 22172 bayes= 10.9763 E= 3.4e-021 103 12 -80 -167 153 -246 -138 -109 -55 154 -1117 -109 103 -246 61 -167 -23 -146 42 49 191 -1117 -1117 -267 -255 -1117 207 -1117 -1117 -1117 214 -1117 197 -1117 -1117 -1117 184 -146 -1117 -1117 -255 54 -238 102 -97 -88 -1117 141 77 -14 -39 -68 25 -1117 152 -267 -255 -1117 -1117 178 184 -1117 -238 -267 -1117 112 -138 49 103 -246 -238 49 125 -1117 -238 32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 23 E= 3.4e-021 0.521739 0.260870 0.130435 0.086957 0.739130 0.043478 0.086957 0.130435 0.173913 0.695652 0.000000 0.130435 0.521739 0.043478 0.347826 0.086957 0.217391 0.086957 0.304348 0.391304 0.956522 0.000000 0.000000 0.043478 0.043478 0.000000 0.956522 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.913043 0.086957 0.000000 0.000000 0.043478 0.347826 0.043478 0.565217 0.130435 0.130435 0.000000 0.739130 0.434783 0.217391 0.173913 0.173913 0.304348 0.000000 0.652174 0.043478 0.043478 0.000000 0.000000 0.956522 0.913043 0.000000 0.043478 0.043478 0.000000 0.521739 0.086957 0.391304 0.521739 0.043478 0.043478 0.391304 0.608696 0.000000 0.043478 0.347826 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC]AC[AG][TGA]AGGAA[TC]T[AC][GA]TA[CT][AT][AT] -------------------------------------------------------------------------------- Time 15.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 31 llr = 362 E-value = 3.4e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2:53:3:12:16114::2::1 pos.-specific C 2:15:15::7:25216::5:2 probability G :a21a528618:152195:75 matrix T 6:2::14112:3313313532 bits 2.1 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 * * * * * Entropy 1.1 * * * * * * (16.9 bits) 0.9 * * * ** * ** 0.6 * ** ***** ***** 0.4 ** *********** ***** 0.2 ********************* 0.0 --------------------- Multilevel TGACGGCGGCGACGACGGTGG consensus A A AT A TT TT TCT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 29007 223 5.11e-10 TCGACATGGA TGAAGGCGGCGTCGGCGGTGT TGGAGAGAGG 41319 149 2.62e-09 GATGCCACAA AGGCGATGGCGACCACGGCGG CATTGAACGC 39424 101 4.06e-08 TCACCGCTGA TGAAGGCTGCGACGTTGATGG GTTGCTCCGT 269961 72 5.31e-08 GGTGAAGTAT CGGCAGCGGCGACGGCGGCGG GTGTCGCAGT 27167 33 7.86e-08 GATAGTAGTG TGGAGGCGGCGATGGTGGCTC CATTGCGGTG 30154 242 8.93e-08 CGTTTGATTG TGTGGGCGGCGTCCACGATGG ATTGGTAAGT 26221 109 1.47e-07 GAGACGAAGG AGACGGCGGCACCATCGTCGG TCGGCACCGG 25949 175 2.10e-07 AGGCTCTTTA CGAGGACGTCGCTGTCGGCGG GGGTGTTGTT 32675 203 3.72e-07 GTGTTGCTCC TGGCGATGGCAAAGCCGTCGG ACTCAAATAT 37628 382 4.16e-07 TTTTCTTGGT TGACGATGGCCTCGTCTGTGG GTGGGCGCGA 24423 292 7.11e-07 GACAACTCTT TGCAGGTGAGGACCATGGCGG TGCTTGTAGC 22535 400 7.89e-07 CAGCGCGATG TGTCGTCGTCGTCGTCGTCGT CGTCGTCGTC 26367 6 9.68e-07 CGTTA CGACGACGGCAACAACGTCTC TGCTCATCGT 26046 242 9.68e-07 TTGTGTTACT TGACGATGGCGATTGTTGTTG TGATGATGAT 28049 302 1.59e-06 CACACGACGG TGAAGGTGAGGACCATGACGT TGCCGCTATC 29217 144 1.92e-06 GTGTTTGGTG TGTCGGTGGTGAGGAGGGTGA TTGGCTGTCA 22476 220 1.92e-06 CGGTGCCGAC CGACGATGGTGCCGCCGTCTC CTTCGTCTCA 19501 82 1.92e-06 GGACATGCAG TGACGTTGATGTTGATGGTTG GGACTGTGAC 23025 259 2.54e-06 CTTCTTCGCG AGCAGGTGAGGACGACGACTG AACCATGGCC 33241 96 3.04e-06 CTGATCGTTG CGGAGGGGACGATTCCGTTGG TATCGTCACC 46 30 3.63e-06 CCAATGTTGG AGAGGGCGGCGAGGAGTGTGT CTAGGCGTTG 24410 54 3.63e-06 ATTCCTGCCT TGACGCCGCTGCTGTCGGTGC TCCTGCTGCT 40387 12 3.96e-06 AAGGTGAGCC TTACGACGTTGACCATGGCGG CCTTTGAGGT 26137 38 5.58e-06 ATGACTTGAA TGTCGCGGACGAAGTTGTTGT TCCACCTTTG 26063 39 5.58e-06 ATCAGTGGCG TGAAGATAGCGATGACGGTCA GCCGTAGCAA 39550 182 7.14e-06 GACGACCTCA TGAAGTGTTCGTCGTCGGTGA AAGATGGGAT 37809 182 7.74e-06 TGCTGCATGC AGAGGGCTGTGAAAGCGGTGC TTGAATCGTT 29955 317 9.08e-06 TGTTGGTGTA CGACGATGGCGTCCTATGTTG ATAGTATTCA 269086 321 1.44e-05 GCCCTCTAGC AGGAGGGGACGAATGCGTCTT CATGGAGTGG 39735 1 1.55e-05 . AGTCGGCGGCACTTTGGATGG ATCGGAAATT 39282 350 2.21e-05 GGAAGTGGAC TGCCGCGAGCGTCAGCGTCGC TTCGACATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 29007 5.1e-10 222_[+2]_257 41319 2.6e-09 148_[+2]_331 39424 4.1e-08 100_[+2]_379 269961 5.3e-08 71_[+2]_408 27167 7.9e-08 32_[+2]_447 30154 8.9e-08 241_[+2]_238 26221 1.5e-07 108_[+2]_371 25949 2.1e-07 174_[+2]_305 32675 3.7e-07 202_[+2]_277 37628 4.2e-07 381_[+2]_98 24423 7.1e-07 291_[+2]_188 22535 7.9e-07 399_[+2]_80 26367 9.7e-07 5_[+2]_474 26046 9.7e-07 241_[+2]_238 28049 1.6e-06 301_[+2]_178 29217 1.9e-06 143_[+2]_336 22476 1.9e-06 219_[+2]_260 19501 1.9e-06 81_[+2]_398 23025 2.5e-06 258_[+2]_221 33241 3e-06 95_[+2]_384 46 3.6e-06 29_[+2]_450 24410 3.6e-06 53_[+2]_426 40387 4e-06 11_[+2]_468 26137 5.6e-06 37_[+2]_442 26063 5.6e-06 38_[+2]_441 39550 7.1e-06 181_[+2]_298 37809 7.7e-06 181_[+2]_298 29955 9.1e-06 316_[+2]_163 269086 1.4e-05 320_[+2]_159 39735 1.5e-05 [+2]_479 39282 2.2e-05 349_[+2]_130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=31 29007 ( 223) TGAAGGCGGCGTCGGCGGTGT 1 41319 ( 149) AGGCGATGGCGACCACGGCGG 1 39424 ( 101) TGAAGGCTGCGACGTTGATGG 1 269961 ( 72) CGGCAGCGGCGACGGCGGCGG 1 27167 ( 33) TGGAGGCGGCGATGGTGGCTC 1 30154 ( 242) TGTGGGCGGCGTCCACGATGG 1 26221 ( 109) AGACGGCGGCACCATCGTCGG 1 25949 ( 175) CGAGGACGTCGCTGTCGGCGG 1 32675 ( 203) TGGCGATGGCAAAGCCGTCGG 1 37628 ( 382) TGACGATGGCCTCGTCTGTGG 1 24423 ( 292) TGCAGGTGAGGACCATGGCGG 1 22535 ( 400) TGTCGTCGTCGTCGTCGTCGT 1 26367 ( 6) CGACGACGGCAACAACGTCTC 1 26046 ( 242) TGACGATGGCGATTGTTGTTG 1 28049 ( 302) TGAAGGTGAGGACCATGACGT 1 29217 ( 144) TGTCGGTGGTGAGGAGGGTGA 1 22476 ( 220) CGACGATGGTGCCGCCGTCTC 1 19501 ( 82) TGACGTTGATGTTGATGGTTG 1 23025 ( 259) AGCAGGTGAGGACGACGACTG 1 33241 ( 96) CGGAGGGGACGATTCCGTTGG 1 46 ( 30) AGAGGGCGGCGAGGAGTGTGT 1 24410 ( 54) TGACGCCGCTGCTGTCGGTGC 1 40387 ( 12) TTACGACGTTGACCATGGCGG 1 26137 ( 38) TGTCGCGGACGAAGTTGTTGT 1 26063 ( 39) TGAAGATAGCGATGACGGTCA 1 39550 ( 182) TGAAGTGTTCGTCGTCGGTGA 1 37809 ( 182) AGAGGGCTGTGAAAGCGGTGC 1 29955 ( 317) CGACGATGGCGTCCTATGTTG 1 269086 ( 321) AGGAGGGGACGAATGCGTCTT 1 39735 ( 1) AGTCGGCGGCACTTTGGATGG 1 39282 ( 350) TGCCGCGAGCGTCAGCGTCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22080 bayes= 10.1813 E= 3.4e-017 -18 -31 -1160 106 -1160 -1160 209 -310 110 -131 -23 -78 34 119 -82 -1160 -298 -1160 209 -1160 34 -131 109 -152 -1160 91 -49 48 -198 -1160 188 -152 -18 -289 143 -111 -1160 157 -123 -52 -98 -289 188 -1160 119 -57 -1160 -11 -98 119 -182 -11 -98 -31 127 -111 48 -131 -1 21 -298 135 -123 -11 -1160 -1160 194 -111 -66 -1160 127 6 -1160 101 -1160 89 -1160 -289 164 -11 -140 -31 118 -52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 3.4e-017 0.225806 0.193548 0.000000 0.580645 0.000000 0.000000 0.967742 0.032258 0.548387 0.096774 0.193548 0.161290 0.322581 0.548387 0.129032 0.000000 0.032258 0.000000 0.967742 0.000000 0.322581 0.096774 0.483871 0.096774 0.000000 0.451613 0.161290 0.387097 0.064516 0.000000 0.838710 0.096774 0.225806 0.032258 0.612903 0.129032 0.000000 0.709677 0.096774 0.193548 0.129032 0.032258 0.838710 0.000000 0.580645 0.161290 0.000000 0.258065 0.129032 0.548387 0.064516 0.258065 0.129032 0.193548 0.548387 0.129032 0.354839 0.096774 0.225806 0.322581 0.032258 0.612903 0.096774 0.258065 0.000000 0.000000 0.870968 0.129032 0.161290 0.000000 0.548387 0.290323 0.000000 0.483871 0.000000 0.516129 0.000000 0.032258 0.709677 0.258065 0.096774 0.193548 0.516129 0.193548 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA]GA[CA]G[GA][CT]G[GA]CG[AT][CT]G[ATG][CT]G[GT][TC][GT]G -------------------------------------------------------------------------------- Time 31.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 46 llr = 418 E-value = 5.5e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 32:43422184:4:19 pos.-specific C 439555659128:481 probability G ::::1::::2:2111: matrix T 341::123::4:55:: bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * ** * * (13.1 bits) 0.9 ** ** * ** 0.6 **** ** ***** 0.4 * ************** 0.2 **************** 0.0 ---------------- Multilevel CTCCCCCCCAACTTCA consensus TC AAA T T AC sequence AA C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25949 317 2.03e-07 ACTTGAGTTG CTCAAACTCAACTTCA ATTTTAGCTT 269235 480 2.89e-07 CGAGGATGCT TTCACACCCATCACCA CAACT 28049 271 4.02e-07 CACATGTTCG CCCCATCCCAACTTCA TACCACACAC 26367 48 4.02e-07 TACCACAGAC AACCAACCCAACATCA GCAGCATGCA 802 454 5.50e-07 CAGAAAAAGC CTCACCACCACCTTCA CCGCCACACT 269086 466 8.69e-07 GACAGACAGC TCCCCCCCCGACACCA CACCTCAAAG 21871 477 8.69e-07 ACCCACAATC ACCACACACAACACCA CCATCACC 39424 436 1.57e-06 ACGACATTTC ACCCGCCTCATCTCCA CCTACGACCG 29217 311 1.57e-06 AGGGGACTTT ATCCCCCTCATGTTCA TTATTGAACT 264201 23 1.57e-06 TCATCAACCG TCCACCACCACCTCCA TTATTATCCT 24262 332 2.09e-06 CTGATTTCTA CGCCAACCCATCTCCA AACATCTCAT 268372 361 2.39e-06 CCTCAACTTT CTCAAACTCAACGTCA AGTTGAGGTT 39735 448 2.73e-06 ACCTTTCGAT CTCCCACACAACAGCA TTTCACTCTA 269779 252 2.73e-06 TTGGAGTTTG CTCAACTACAACATCA AGTTGAATGG 19501 413 3.52e-06 GTACTCCACC AACCCACCCACCGCCA AACACAATCG 46 474 6.35e-06 CCATTCCACT CTCACCCACAACTTCC TTGCTTTTGT 22535 481 7.95e-06 CTTCATTCCC TCCCCTTTCATCATCA ATGC 26250 385 8.88e-06 TCTTTCTCTC TCCCCCCTCATCTCTA CCATTGACGA 24410 474 8.88e-06 ATACACCCCT CTCCCCTCAACCACCA ACGTTTCAAC 32675 362 1.10e-05 TTGTTGCTGT TGCACACACAACACCA CCACAACTAT 30154 76 1.36e-05 TGTGTCCGCC CTCCAACCAAAGTTCA TCCACCTTCT 29955 468 1.51e-05 CGTACACGTA CACCAACTCATCTTTA AATACTCTCA 27167 234 1.68e-05 AATTCAGCTC TCCCGCCACAACTTAA TTGCCAACTA 37032 87 2.05e-05 AATTGTAAGT ATCAGACTCAACTTAA GTAGACTCTT 29007 468 2.05e-05 ACTGTCTCTT CTCTCCCCAATCTTCA GTTTATCCTA 37809 46 2.26e-05 AACATAAACC CTCTCCCCCACGACCA CCGCTCGCCT 33241 484 2.26e-05 GATGTGTTGC TTCAACTTCAACATAA G 40387 210 3.00e-05 CGAGCCTCTC CCTCCTACCAACATCA AACGACGTCG 27292 472 3.29e-05 GCTGAACCTC CACCCACCCCACTTGA CGACGGCCAA 41319 361 3.60e-05 CGTCAATTTT TCTAACTTCAACTTCA AACCTCTTAC 26046 460 3.94e-05 GACAAACTGA CACCAACCAGCCACCA CACTCCCTCC 40312 450 5.12e-05 CGTCGTCCCG CTCCACCTCGTCAACA CTTGCCGCCG 29825 466 5.12e-05 AAAAGGTCTC TCCACCGCCAACTCGA AGCAGCCACT 39282 53 5.57e-05 AGAACTTTCA ACCACCATCATGGTCA CGCACCTTAA 37628 479 8.39e-05 CCATCCCATT ACTCCATCCGTCATCA TAGGTA 26063 85 8.39e-05 TGCTCTCCTC AACACCACCGCCTGCA CCGATCGATG 40329 445 9.08e-05 TATTACATGG ACCCATCTCATGTCAA TCCTCTTCTC 26221 185 9.08e-05 AGACACCGTT CACCACACCATCGCCC ACATCGCTAT 39550 455 1.54e-04 TAGACACTGT AACCCCTTCCCGTCCA TTCTATCATT 26137 431 1.54e-04 TGCTCACCAC AACAGTCTCACCACAA CTCTTCACTT 269961 408 1.77e-04 ACTAATGAAA CTCAAACACGTATTCA ATTCCCGGTT 23025 224 1.90e-04 GGTGGACAAC CAACCATCCGTCTCCA CCTCTCCCAC 268651 418 2.84e-04 TCTCGCTTGC TACAACAACACGAGCA TTCTTCCTCT 24423 470 3.65e-04 CTCCTTGTCA TCCACAGCACTCTTCA CAACACTAAT 22476 442 4.37e-04 ATGGGACTTC TTTCCTTTCATCATGA ATCAATACCT 31084 157 4.63e-04 TCTCCAGCAC TTCCGCAACAACACAC TGCAAACATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25949 2e-07 316_[+3]_168 269235 2.9e-07 479_[+3]_5 28049 4e-07 270_[+3]_214 26367 4e-07 47_[+3]_437 802 5.5e-07 453_[+3]_31 269086 8.7e-07 465_[+3]_19 21871 8.7e-07 476_[+3]_8 39424 1.6e-06 435_[+3]_49 29217 1.6e-06 310_[+3]_174 264201 1.6e-06 22_[+3]_462 24262 2.1e-06 331_[+3]_153 268372 2.4e-06 360_[+3]_124 39735 2.7e-06 447_[+3]_37 269779 2.7e-06 251_[+3]_233 19501 3.5e-06 412_[+3]_72 46 6.4e-06 473_[+3]_11 22535 8e-06 480_[+3]_4 26250 8.9e-06 384_[+3]_100 24410 8.9e-06 473_[+3]_11 32675 1.1e-05 361_[+3]_123 30154 1.4e-05 75_[+3]_409 29955 1.5e-05 467_[+3]_17 27167 1.7e-05 233_[+3]_251 37032 2e-05 86_[+3]_398 29007 2e-05 467_[+3]_17 37809 2.3e-05 45_[+3]_439 33241 2.3e-05 483_[+3]_1 40387 3e-05 209_[+3]_275 27292 3.3e-05 471_[+3]_13 41319 3.6e-05 360_[+3]_124 26046 3.9e-05 459_[+3]_25 40312 5.1e-05 449_[+3]_35 29825 5.1e-05 465_[+3]_19 39282 5.6e-05 52_[+3]_432 37628 8.4e-05 478_[+3]_6 26063 8.4e-05 84_[+3]_400 40329 9.1e-05 444_[+3]_40 26221 9.1e-05 184_[+3]_300 39550 0.00015 454_[+3]_30 26137 0.00015 430_[+3]_54 269961 0.00018 407_[+3]_77 23025 0.00019 223_[+3]_261 268651 0.00028 417_[+3]_67 24423 0.00036 469_[+3]_15 22476 0.00044 441_[+3]_43 31084 0.00046 156_[+3]_328 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=46 25949 ( 317) CTCAAACTCAACTTCA 1 269235 ( 480) TTCACACCCATCACCA 1 28049 ( 271) CCCCATCCCAACTTCA 1 26367 ( 48) AACCAACCCAACATCA 1 802 ( 454) CTCACCACCACCTTCA 1 269086 ( 466) TCCCCCCCCGACACCA 1 21871 ( 477) ACCACACACAACACCA 1 39424 ( 436) ACCCGCCTCATCTCCA 1 29217 ( 311) ATCCCCCTCATGTTCA 1 264201 ( 23) TCCACCACCACCTCCA 1 24262 ( 332) CGCCAACCCATCTCCA 1 268372 ( 361) CTCAAACTCAACGTCA 1 39735 ( 448) CTCCCACACAACAGCA 1 269779 ( 252) CTCAACTACAACATCA 1 19501 ( 413) AACCCACCCACCGCCA 1 46 ( 474) CTCACCCACAACTTCC 1 22535 ( 481) TCCCCTTTCATCATCA 1 26250 ( 385) TCCCCCCTCATCTCTA 1 24410 ( 474) CTCCCCTCAACCACCA 1 32675 ( 362) TGCACACACAACACCA 1 30154 ( 76) CTCCAACCAAAGTTCA 1 29955 ( 468) CACCAACTCATCTTTA 1 27167 ( 234) TCCCGCCACAACTTAA 1 37032 ( 87) ATCAGACTCAACTTAA 1 29007 ( 468) CTCTCCCCAATCTTCA 1 37809 ( 46) CTCTCCCCCACGACCA 1 33241 ( 484) TTCAACTTCAACATAA 1 40387 ( 210) CCTCCTACCAACATCA 1 27292 ( 472) CACCCACCCCACTTGA 1 41319 ( 361) TCTAACTTCAACTTCA 1 26046 ( 460) CACCAACCAGCCACCA 1 40312 ( 450) CTCCACCTCGTCAACA 1 29825 ( 466) TCCACCGCCAACTCGA 1 39282 ( 53) ACCACCATCATGGTCA 1 37628 ( 479) ACTCCATCCGTCATCA 1 26063 ( 85) AACACCACCGCCTGCA 1 40329 ( 445) ACCCATCTCATGTCAA 1 26221 ( 185) CACCACACCATCGCCC 1 39550 ( 455) AACCCCTTCCCGTCCA 1 26137 ( 431) AACAGTCTCACCACAA 1 269961 ( 408) CTCAAACACGTATTCA 1 23025 ( 224) CAACCATCCGTCTCCA 1 268651 ( 418) TACAACAACACGAGCA 1 24423 ( 470) TCCACAGCACTCTTCA 1 22476 ( 442) TTTCCTTTCATCATGA 1 31084 ( 157) TTCCGCAACAACACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22310 bayes= 9.32214 E= 5.5e-019 3 86 -1217 13 -9 44 -238 49 -355 189 -1217 -168 69 118 -1217 -267 45 118 -106 -1217 62 100 -1217 -109 -55 129 -238 -51 -38 93 -1217 32 -123 189 -1217 -1217 162 -188 -58 -1217 69 -14 -1217 41 -355 178 -58 -1217 69 -1217 -139 85 -355 78 -180 85 -97 167 -180 -267 187 -188 -1217 -1217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 46 E= 5.5e-019 0.260870 0.434783 0.000000 0.304348 0.239130 0.326087 0.043478 0.391304 0.021739 0.891304 0.000000 0.086957 0.413043 0.543478 0.000000 0.043478 0.347826 0.543478 0.108696 0.000000 0.391304 0.478261 0.000000 0.130435 0.173913 0.586957 0.043478 0.195652 0.195652 0.456522 0.000000 0.347826 0.108696 0.891304 0.000000 0.000000 0.782609 0.065217 0.152174 0.000000 0.413043 0.217391 0.000000 0.369565 0.021739 0.826087 0.152174 0.000000 0.413043 0.000000 0.086957 0.500000 0.021739 0.413043 0.065217 0.500000 0.130435 0.760870 0.065217 0.043478 0.934783 0.065217 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CTA][TCA]C[CA][CA][CA]C[CT]CA[ATC]C[TA][TC]CA -------------------------------------------------------------------------------- Time 47.56 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19501 3.33e-08 81_[+2(1.92e-06)]_67_[+1(3.36e-05)]_\ 138_[+1(1.54e-07)]_67_[+3(3.52e-06)]_72 21871 9.09e-03 476_[+3(8.69e-07)]_8 22476 2.48e-03 132_[+2(9.82e-06)]_19_\ [+2(1.33e-05)]_26_[+2(1.92e-06)]_260 22535 1.85e-09 54_[+1(7.20e-09)]_208_\ [+2(3.79e-05)]_97_[+2(7.89e-07)]_[+2(2.11e-06)]_39_[+3(7.95e-06)]_4 23025 2.26e-07 151_[+1(1.84e-08)]_88_\ [+2(2.54e-06)]_221 24262 7.84e-06 219_[+1(1.54e-07)]_93_\ [+3(2.09e-06)]_153 24410 9.77e-07 53_[+2(3.63e-06)]_205_\ [+1(1.33e-06)]_115_[+3(5.12e-05)]_44_[+3(8.88e-06)]_11 24423 1.68e-06 183_[+1(3.27e-07)]_89_\ [+2(7.11e-07)]_188 25949 1.11e-06 174_[+2(2.10e-07)]_121_\ [+3(2.03e-07)]_168 26046 6.41e-07 241_[+2(9.68e-07)]_122_\ [+1(7.09e-07)]_13_[+3(8.39e-05)]_27_[+3(3.94e-05)]_25 26063 3.01e-06 38_[+2(5.58e-06)]_25_[+3(8.39e-05)]_\ 225_[+1(3.27e-07)]_156 26137 1.01e-03 37_[+2(5.58e-06)]_442 26221 1.13e-04 108_[+2(1.47e-07)]_55_\ [+3(9.08e-05)]_300 26250 5.76e-06 82_[+1(3.42e-08)]_283_\ [+3(8.88e-06)]_100 26367 4.76e-10 5_[+2(9.68e-07)]_21_[+3(4.02e-07)]_\ 261_[+1(2.68e-08)]_157 264201 3.17e-03 22_[+3(1.57e-06)]_462 268372 5.76e-05 44_[+1(9.77e-07)]_297_\ [+3(2.39e-06)]_104_[+1(3.85e-05)]_1 268651 2.90e-01 500 269086 1.41e-04 320_[+2(1.44e-05)]_124_\ [+3(8.69e-07)]_19 269235 3.72e-06 348_[+1(6.02e-07)]_112_\ [+3(2.89e-07)]_5 269779 4.65e-05 251_[+3(2.73e-06)]_62_\ [+1(1.33e-06)]_152 269961 1.21e-08 71_[+2(5.31e-08)]_283_\ [+1(3.83e-08)]_106 27167 4.20e-09 32_[+2(7.86e-08)]_180_\ [+3(1.68e-05)]_56_[+2(2.06e-05)]_85_[+1(8.34e-08)]_70 27292 1.75e-04 238_[+1(2.99e-07)]_4_[+1(8.45e-06)]_\ 96_[+1(4.39e-05)]_76_[+3(3.29e-05)]_13 28049 8.27e-09 225_[+1(3.58e-07)]_26_\ [+3(4.02e-07)]_15_[+2(1.59e-06)]_178 29007 1.58e-07 222_[+2(5.11e-10)]_224_\ [+3(2.05e-05)]_17 29217 2.27e-08 16_[+1(7.78e-05)]_108_\ [+2(1.92e-06)]_75_[+1(2.27e-07)]_52_[+3(1.57e-06)]_101_[+3(9.08e-05)]_57 29825 4.28e-02 465_[+3(5.12e-05)]_19 29955 1.89e-03 316_[+2(9.08e-06)]_130_\ [+3(1.51e-05)]_17 30154 2.12e-09 14_[+1(4.31e-08)]_42_[+3(1.36e-05)]_\ 36_[+2(5.58e-06)]_93_[+2(8.93e-08)]_63_[+3(3.94e-05)]_159 31084 2.87e-01 500 32675 9.87e-05 202_[+2(3.72e-07)]_37_\ [+2(9.08e-06)]_80_[+3(1.10e-05)]_123 33241 9.13e-04 95_[+2(3.04e-06)]_367_\ [+3(2.26e-05)]_1 37032 3.14e-04 86_[+3(2.05e-05)]_143_\ [+3(8.39e-05)]_36_[+1(9.04e-07)]_184 37628 1.63e-04 3_[+2(8.84e-05)]_278_[+2(5.20e-05)]_\ 58_[+2(4.16e-07)]_76_[+3(8.39e-05)]_6 37809 2.20e-03 45_[+3(2.26e-05)]_120_\ [+2(7.74e-06)]_298 39282 8.26e-03 52_[+3(5.57e-05)]_281_\ [+2(2.21e-05)]_130 39424 1.13e-06 100_[+2(4.06e-08)]_314_\ [+3(1.57e-06)]_49 39550 8.28e-03 181_[+2(7.14e-06)]_298 39735 1.84e-06 [+2(1.55e-05)]_132_[+1(2.06e-06)]_\ 275_[+3(2.73e-06)]_37 40312 1.84e-01 449_[+3(5.12e-05)]_35 40329 2.00e-01 444_[+3(9.08e-05)]_40 40387 4.27e-04 11_[+2(3.96e-06)]_122_\ [+2(9.35e-05)]_34_[+3(3.00e-05)]_275 41319 8.06e-09 148_[+2(2.62e-09)]_191_\ [+3(3.60e-05)]_27_[+1(2.37e-06)]_78 46 4.59e-04 29_[+2(3.63e-06)]_423_\ [+3(6.35e-06)]_11 802 6.51e-07 383_[+1(4.84e-08)]_51_\ [+3(5.50e-07)]_31 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************