******************************************************************************** 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/140/140.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11320 1.0000 500 11659 1.0000 500 11680 1.0000 500 12292 1.0000 500 16952 1.0000 500 1713 1.0000 500 21045 1.0000 500 22409 1.0000 500 24364 1.0000 500 24389 1.0000 500 25695 1.0000 500 263836 1.0000 500 264759 1.0000 500 269573 1.0000 500 32944 1.0000 500 41583 1.0000 500 6605 1.0000 500 8409 1.0000 500 8880 1.0000 500 8999 1.0000 500 9218 1.0000 500 9262 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/140/140.seqs.fa -oc motifs/140 -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= 22 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= 11000 N= 22 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.225 G 0.232 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.225 G 0.232 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 22 llr = 225 E-value = 8.4e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2:::213::1::3411 pos.-specific C 3:142::::3::::1: probability G :19315:19::a233: matrix T 59:35479:6a:5359 bits 2.2 * 1.9 * 1.7 * 1.5 ** * ** * Relative 1.3 ** ** ** * Entropy 1.1 ** ** ** * (14.8 bits) 0.9 ** *** ** * 0.6 ** ******* * 0.4 ** ******** * 0.2 **************** 0.0 ---------------- Multilevel TTGCTGTTGTTGTATT consensus C GATA C ATG sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 24389 281 2.31e-08 TAGAGCAGTG TTGTTGTTGTTGTTGT TGTTGCAACT 9262 223 5.08e-08 ATGATGACGA TTGTTGTTGCTGTTTT GTGGAGCGAA 1713 201 1.41e-07 AGGCTCACGC TTGGTTTTGTTGATTT GACGTCTACA 8880 226 2.04e-07 CGTGGTGGAT TTGCCTTTGTTGAATT TAGAGAATGT 11659 226 2.04e-07 CGTGGTGGAT TTGCCTTTGTTGAATT TAGAGAATGT 16952 75 6.74e-07 TTTCTCATCG CTGCGTTTGCTGTAGT TTCCGTTGAT 6605 168 1.26e-06 GGAGTTCGTT TGGCTGTTGTTGAAGT AGATACAATA 8409 152 2.78e-06 GGAACGTCCC ATGTCGTTGTTGGTGT TGCGAGAGTG 21045 351 3.79e-06 CTTACGTTTT CTCCTGATGTTGATTT CCGTCGGAGA 9218 215 5.10e-06 GCGTGTACTT CTGCTTTTGTTGTGCA AATTTGACAC 11320 238 5.61e-06 GGCGAGTGTG TTGGCTTTGTTGACGT CGCCTGTCGG 8999 116 8.86e-06 CCCGATAGAC TTGGATTGGCTGGATT GATGAGTGTA 25695 393 1.24e-05 TGCTTGAGAG ATGGAATTGTTGGTTT CGCTCCTTCG 264759 256 1.46e-05 TTGGGCGAGG CTGTGGAGGCTGTATT ATGTAAGAAT 263836 256 1.46e-05 TTGGGCGAGG CTGTGGAGGCTGTATT ATGTAAGAAT 32944 303 1.71e-05 GGCAAAGTAT TTGGTATTGCTGGGAT CCCAGGTGAT 22409 437 2.67e-05 ACACGATCCT TTGCATATCTTGTGCT CGCATTGATA 269573 180 3.30e-05 GATGATGATG ATGATGATGATGTGTT CTCTTTAGCT 41583 166 3.53e-05 GGAGGCATCG CTGCAGTTGCAGTGAT GTGTTTCGAT 24364 475 7.09e-05 GAGCATCCAT GGGGTGTTGTTGTGGA GGCATCTAAT 12292 58 8.42e-05 TCTTTTTCGA ATCCTTCTGATGTAGT ACATATTTCA 11680 98 1.17e-04 TTTGACCTTT TTCTAGATATTGTTCT AATGGAAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24389 2.3e-08 280_[+1]_204 9262 5.1e-08 222_[+1]_262 1713 1.4e-07 200_[+1]_284 8880 2e-07 225_[+1]_259 11659 2e-07 225_[+1]_259 16952 6.7e-07 74_[+1]_410 6605 1.3e-06 167_[+1]_317 8409 2.8e-06 151_[+1]_333 21045 3.8e-06 350_[+1]_134 9218 5.1e-06 214_[+1]_270 11320 5.6e-06 237_[+1]_247 8999 8.9e-06 115_[+1]_369 25695 1.2e-05 392_[+1]_92 264759 1.5e-05 255_[+1]_229 263836 1.5e-05 255_[+1]_229 32944 1.7e-05 302_[+1]_182 22409 2.7e-05 436_[+1]_48 269573 3.3e-05 179_[+1]_305 41583 3.5e-05 165_[+1]_319 24364 7.1e-05 474_[+1]_10 12292 8.4e-05 57_[+1]_427 11680 0.00012 97_[+1]_387 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=22 24389 ( 281) TTGTTGTTGTTGTTGT 1 9262 ( 223) TTGTTGTTGCTGTTTT 1 1713 ( 201) TTGGTTTTGTTGATTT 1 8880 ( 226) TTGCCTTTGTTGAATT 1 11659 ( 226) TTGCCTTTGTTGAATT 1 16952 ( 75) CTGCGTTTGCTGTAGT 1 6605 ( 168) TGGCTGTTGTTGAAGT 1 8409 ( 152) ATGTCGTTGTTGGTGT 1 21045 ( 351) CTCCTGATGTTGATTT 1 9218 ( 215) CTGCTTTTGTTGTGCA 1 11320 ( 238) TTGGCTTTGTTGACGT 1 8999 ( 116) TTGGATTGGCTGGATT 1 25695 ( 393) ATGGAATTGTTGGTTT 1 264759 ( 256) CTGTGGAGGCTGTATT 1 263836 ( 256) CTGTGGAGGCTGTATT 1 32944 ( 303) TTGGTATTGCTGGGAT 1 22409 ( 437) TTGCATATCTTGTGCT 1 269573 ( 180) ATGATGATGATGTGTT 1 41583 ( 166) CTGCAGTTGCAGTGAT 1 24364 ( 475) GGGGTGTTGTTGTGGA 1 12292 ( 58) ATCCTTCTGATGTAGT 1 11680 ( 98) TTCTAGATATTGTTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10670 bayes= 9.27461 E= 8.4e-009 -56 28 -235 87 -1110 -1110 -135 173 -1110 -72 189 -1110 -256 86 23 -1 -24 -30 -77 73 -156 -1110 110 58 2 -230 -1110 131 -1110 -1110 -77 166 -256 -230 197 -1110 -156 50 -1110 111 -256 -1110 -1110 180 -1110 -1110 210 -1110 2 -1110 -35 99 44 -230 23 22 -156 -72 45 73 -156 -1110 -1110 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 22 E= 8.4e-009 0.181818 0.272727 0.045455 0.500000 0.000000 0.000000 0.090909 0.909091 0.000000 0.136364 0.863636 0.000000 0.045455 0.409091 0.272727 0.272727 0.227273 0.181818 0.136364 0.454545 0.090909 0.000000 0.500000 0.409091 0.272727 0.045455 0.000000 0.681818 0.000000 0.000000 0.136364 0.863636 0.045455 0.045455 0.909091 0.000000 0.090909 0.318182 0.000000 0.590909 0.045455 0.000000 0.000000 0.954545 0.000000 0.000000 1.000000 0.000000 0.272727 0.000000 0.181818 0.545455 0.363636 0.045455 0.272727 0.318182 0.090909 0.136364 0.318182 0.454545 0.090909 0.000000 0.000000 0.909091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]TG[CGT][TA][GT][TA]TG[TC]TG[TA][ATG][TG]T -------------------------------------------------------------------------------- Time 5.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 19 llr = 227 E-value = 9.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 113164233791222161221 pos.-specific C :1:2:22::1::12::2:1:2 probability G 772744277218332827727 matrix T 216::14::::25371:2171 bits 2.2 1.9 1.7 1.5 * Relative 1.3 * * * Entropy 1.1 * ** ** ** * * (17.2 bits) 0.9 ** ** ***** * ** * 0.6 ** ** ***** ******* 0.4 ***** ***** ******* 0.2 ****** ****** ******* 0.0 --------------------- Multilevel GGTGAGTGGAAGTGTGAGGTG consensus T ACGAAAAG GT CTA C sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8880 422 7.14e-10 AGCTATCTTC GGTGAGAAGAAGTTTGAGGTC AACAGCTAAA 11659 422 7.14e-10 AGCTATCTTC GGTGAGAAGAAGTTTGAGGTC AACAGCTAAA 16952 337 1.86e-09 AAAGGAGCAA GCAGAATGGAAGGGTGAGGTG GTGGGAGAGA 41583 109 1.52e-08 GAGAAATTCT GGTGGGTAGAAGATTGCGATG CGTAAAAGAC 9262 19 1.94e-07 ACTGTTTTGG GGAGAGAGAGAGTGAGAGGAG TTATTGACGA 264759 111 2.38e-07 CCATAGCTTA GTGGAAGGGAAGGTGGCGGTG GTATCAACAG 263836 111 2.38e-07 CCATAGCTTA GTGGAAGGGAAGGTGGCGGTG GTATCAACAG 11320 258 3.93e-07 TGACGTCGCC TGTCGGCGGAATTCTGAGGGG CGTCTAAAAG 9218 175 9.17e-07 GAGCGGAGAG GGTGGGTGAAAGAAATAGATG GTCTCCCTCG 269573 226 9.17e-07 CAGCGTTGGA GGTGAAGAAAAGTGTGATAGC TGATCCCGCG 21045 116 9.17e-07 AAGCGAACGG AGAGGCTGGGAGGATGGGGTG CCTTTGATCG 24389 236 2.38e-06 TGCTGCTGCT GCTGGACGGAAGGATGCGATA GCGAGTGACT 6605 141 4.51e-06 AGTGGGAGGT GGGAGGGAGAAGAGAGAGGAG TTCGTTTGGC 11680 463 6.58e-06 GAAAGCAGAT TGAGGTTGGAATTGTGAAGTC TCGAGTGAGA 8999 292 1.54e-05 TGCCACCAGT TGTGGAAGGGAGCTTGGTTTG AACCATGCCT 1713 20 1.64e-05 CACGAACCTT GGTCACTGAAAGTGGAAGCGG TGAGAGGCAA 24364 270 1.88e-05 GCTGCCACTT TGTCAACAACAGTCTGGTGTG AGCGACGGAC 22409 364 1.88e-05 ATACAAGTAT GGTGAGTGGGGATCTGATGTT TTGCCTTTGC 25695 15 2.00e-05 TCTACTACAG GAACACTGGAATTATTAGGAG AAACATCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8880 7.1e-10 421_[+2]_58 11659 7.1e-10 421_[+2]_58 16952 1.9e-09 336_[+2]_143 41583 1.5e-08 108_[+2]_371 9262 1.9e-07 18_[+2]_461 264759 2.4e-07 110_[+2]_369 263836 2.4e-07 110_[+2]_369 11320 3.9e-07 257_[+2]_222 9218 9.2e-07 174_[+2]_305 269573 9.2e-07 225_[+2]_254 21045 9.2e-07 115_[+2]_364 24389 2.4e-06 235_[+2]_244 6605 4.5e-06 140_[+2]_339 11680 6.6e-06 462_[+2]_17 8999 1.5e-05 291_[+2]_188 1713 1.6e-05 19_[+2]_460 24364 1.9e-05 269_[+2]_210 22409 1.9e-05 363_[+2]_116 25695 2e-05 14_[+2]_465 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=19 8880 ( 422) GGTGAGAAGAAGTTTGAGGTC 1 11659 ( 422) GGTGAGAAGAAGTTTGAGGTC 1 16952 ( 337) GCAGAATGGAAGGGTGAGGTG 1 41583 ( 109) GGTGGGTAGAAGATTGCGATG 1 9262 ( 19) GGAGAGAGAGAGTGAGAGGAG 1 264759 ( 111) GTGGAAGGGAAGGTGGCGGTG 1 263836 ( 111) GTGGAAGGGAAGGTGGCGGTG 1 11320 ( 258) TGTCGGCGGAATTCTGAGGGG 1 9218 ( 175) GGTGGGTGAAAGAAATAGATG 1 269573 ( 226) GGTGAAGAAAAGTGTGATAGC 1 21045 ( 116) AGAGGCTGGGAGGATGGGGTG 1 24389 ( 236) GCTGGACGGAAGGATGCGATA 1 6605 ( 141) GGGAGGGAGAAGAGAGAGGAG 1 11680 ( 463) TGAGGTTGGAATTGTGAAGTC 1 8999 ( 292) TGTGGAAGGGAGCTTGGTTTG 1 1713 ( 20) GGTCACTGAAAGTGGAAGCGG 1 24364 ( 270) TGTCAACAACAGTCTGGTGTG 1 22409 ( 364) GGTGAGTGGGGATCTGATGTT 1 25695 ( 15) GAACACTGGAATTATTAGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10560 bayes= 9.31094 E= 9.1e-005 -235 -1089 166 -38 -235 -109 166 -138 -3 -1089 -56 108 -235 -9 166 -1089 111 -1089 86 -1089 45 -51 86 -238 -35 -51 -14 62 23 -1089 156 -1089 -3 -1089 166 -1089 145 -209 -14 -1089 182 -1089 -214 -1089 -235 -1089 176 -80 -77 -209 18 94 -35 -51 44 20 -77 -1089 -56 132 -235 -1089 186 -138 123 -9 -56 -1089 -235 -1089 166 -38 -35 -209 156 -238 -77 -1089 -56 132 -235 -9 156 -238 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 19 E= 9.1e-005 0.052632 0.000000 0.736842 0.210526 0.052632 0.105263 0.736842 0.105263 0.263158 0.000000 0.157895 0.578947 0.052632 0.210526 0.736842 0.000000 0.578947 0.000000 0.421053 0.000000 0.368421 0.157895 0.421053 0.052632 0.210526 0.157895 0.210526 0.421053 0.315789 0.000000 0.684211 0.000000 0.263158 0.000000 0.736842 0.000000 0.736842 0.052632 0.210526 0.000000 0.947368 0.000000 0.052632 0.000000 0.052632 0.000000 0.789474 0.157895 0.157895 0.052632 0.263158 0.526316 0.210526 0.157895 0.315789 0.315789 0.157895 0.000000 0.157895 0.684211 0.052632 0.000000 0.842105 0.105263 0.631579 0.210526 0.157895 0.000000 0.052632 0.000000 0.736842 0.210526 0.210526 0.052632 0.684211 0.052632 0.157895 0.000000 0.157895 0.684211 0.052632 0.210526 0.684211 0.052632 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]G[TA][GC][AG][GA][TAG][GA][GA][AG]AG[TG][GTA]TG[AC][GT][GA]T[GC] -------------------------------------------------------------------------------- Time 10.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 20 llr = 232 E-value = 7.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 454254:92:56:57:93533 pos.-specific C 656932a:36314439:3475 probability G 1:::1::12132:2:::3111 matrix T :11:251:54:26:11121:3 bits 2.2 1.9 * 1.7 * * 1.5 * ** ** Relative 1.3 * ** ** Entropy 1.1 * ** * ** (16.8 bits) 0.9 *** ** * * ** * 0.6 **** ** * ***** * 0.4 **** *** ******** ** 0.2 ***************** *** 0.0 --------------------- Multilevel CCCCATCATCAATAACAAACC consensus AAA CA CTGTCCC CCAA sequence C C G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9262 450 9.92e-12 CAAATCCAAT CACCATCATCAATAACACACC TCATACAAAC 11320 478 1.76e-09 TGGATGGGAA CCCCATCACCCATCACACAAC AA 8880 1 1.64e-07 . CAACAACAACAACAACAACAT CATCAAACAA 11659 1 1.64e-07 . CAACAACAACAACAACAACAT CATCAAACAA 1713 453 4.16e-07 AACACACATC GCACATCATCATTACCAACCA TTAAATCACG 16952 428 4.64e-07 AATACCGAGA ACACCACACTCACCACATACA AGAACACATA 8409 393 6.37e-07 TTGAACCCCC CCCCACCAGCAGTCACATTCC TTGTCACGCT 24389 302 6.37e-07 GTTGTTGTTG CAACTCCATCCATGACATCCA CAGTACTGCT 24364 322 6.37e-07 GATAATGATG CACCGTCATCGACAACAGCAG CAGCAGCTTC 6605 473 8.64e-07 TGACATGAGA ACACAACACCAGCAACTCACC AATCACC 9218 331 1.54e-06 CTACAATCCT CCCCCATATTAATACCACACT ATCCAATCCT 11680 166 2.62e-06 AGTCATCTCT CACCCCCACTCCCAACATCCT CTTCTACTTC 264759 70 3.65e-06 ACTCGATCCG AACAAACATTGATCCTAGACC AAATTGCACA 263836 70 3.65e-06 ACTCGATCCG AACAAACATTGATCCTAGACC AAATTGCACA 22409 119 4.64e-06 ATCTGTGTAT GCCCCTCGTCATTCACAGGCA ACAACAGACC 269573 48 9.75e-06 TTGACATATA CACCATCAACCGTCTCAAAGT ACCCATAGAG 21045 282 1.46e-05 TCTAGTTTTA ACCCCTCAGGATTAACAAGAA AAATCAAGTG 32944 426 2.13e-05 ATGAAACCTT ACTATTCAGTGATGACAAACC GCACGTCCAT 8999 438 2.41e-05 CAACGTGACA ACACGTCGCCGTCGCCACCAC TCCACTACAT 12292 299 2.55e-05 CAATTTGCGT CTCCTCCATTGACCTCTGCCC ACCATTGTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9262 9.9e-12 449_[+3]_30 11320 1.8e-09 477_[+3]_2 8880 1.6e-07 [+3]_479 11659 1.6e-07 [+3]_479 1713 4.2e-07 452_[+3]_27 16952 4.6e-07 427_[+3]_52 8409 6.4e-07 392_[+3]_87 24389 6.4e-07 301_[+3]_178 24364 6.4e-07 321_[+3]_158 6605 8.6e-07 472_[+3]_7 9218 1.5e-06 330_[+3]_149 11680 2.6e-06 165_[+3]_314 264759 3.7e-06 69_[+3]_410 263836 3.7e-06 69_[+3]_410 22409 4.6e-06 118_[+3]_361 269573 9.7e-06 47_[+3]_432 21045 1.5e-05 281_[+3]_198 32944 2.1e-05 425_[+3]_54 8999 2.4e-05 437_[+3]_42 12292 2.6e-05 298_[+3]_181 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=20 9262 ( 450) CACCATCATCAATAACACACC 1 11320 ( 478) CCCCATCACCCATCACACAAC 1 8880 ( 1) CAACAACAACAACAACAACAT 1 11659 ( 1) CAACAACAACAACAACAACAT 1 1713 ( 453) GCACATCATCATTACCAACCA 1 16952 ( 428) ACACCACACTCACCACATACA 1 8409 ( 393) CCCCACCAGCAGTCACATTCC 1 24389 ( 302) CAACTCCATCCATGACATCCA 1 24364 ( 322) CACCGTCATCGACAACAGCAG 1 6605 ( 473) ACACAACACCAGCAACTCACC 1 9218 ( 331) CCCCCATATTAATACCACACT 1 11680 ( 166) CACCCCCACTCCCAACATCCT 1 264759 ( 70) AACAAACATTGATCCTAGACC 1 263836 ( 70) AACAAACATTGATCCTAGACC 1 22409 ( 119) GCCCCTCGTCATTCACAGGCA 1 269573 ( 48) CACCATCAACCGTCTCAAAGT 1 21045 ( 282) ACCCCTCAGGATTAACAAGAA 1 32944 ( 426) ACTATTCAGTGATGACAAACC 1 8999 ( 438) ACACGTCGCCGTCGCCACCAC 1 12292 ( 299) CTCCTCCATTGACCTCTGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10560 bayes= 9.29364 E= 7.2e-006 38 129 -122 -1097 74 115 -1097 -245 38 142 -1097 -245 -84 192 -1097 -1097 90 15 -122 -87 38 -17 -1097 72 -1097 208 -1097 -245 174 -1097 -122 -1097 -84 15 -63 72 -1097 142 -221 35 74 15 37 -1097 116 -217 -63 -45 -1097 83 -1097 113 74 83 -63 -1097 127 15 -1097 -145 -1097 200 -1097 -145 174 -1097 -1097 -145 16 15 10 -45 74 83 -122 -245 16 153 -221 -1097 -10 100 -221 -13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 7.2e-006 0.350000 0.550000 0.100000 0.000000 0.450000 0.500000 0.000000 0.050000 0.350000 0.600000 0.000000 0.050000 0.150000 0.850000 0.000000 0.000000 0.500000 0.250000 0.100000 0.150000 0.350000 0.200000 0.000000 0.450000 0.000000 0.950000 0.000000 0.050000 0.900000 0.000000 0.100000 0.000000 0.150000 0.250000 0.150000 0.450000 0.000000 0.600000 0.050000 0.350000 0.450000 0.250000 0.300000 0.000000 0.600000 0.050000 0.150000 0.200000 0.000000 0.400000 0.000000 0.600000 0.450000 0.400000 0.150000 0.000000 0.650000 0.250000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.900000 0.000000 0.000000 0.100000 0.300000 0.250000 0.250000 0.200000 0.450000 0.400000 0.100000 0.050000 0.300000 0.650000 0.050000 0.000000 0.250000 0.450000 0.050000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA][CA][CA]C[AC][TAC]CA[TC][CT][AGC][AT][TC][AC][AC]CA[ACGT][AC][CA][CAT] -------------------------------------------------------------------------------- Time 14.80 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11320 1.89e-10 237_[+1(5.61e-06)]_4_[+2(3.93e-07)]_\ 199_[+3(1.76e-09)]_2 11659 1.60e-12 [+3(1.64e-07)]_204_[+1(2.04e-07)]_\ 180_[+2(7.14e-10)]_58 11680 2.92e-05 165_[+3(2.62e-06)]_276_\ [+2(6.58e-06)]_17 12292 9.74e-03 57_[+1(8.42e-05)]_225_\ [+3(2.55e-05)]_181 16952 3.21e-11 74_[+1(6.74e-07)]_246_\ [+2(1.86e-09)]_70_[+3(4.64e-07)]_23_[+3(2.27e-05)]_8 1713 3.08e-08 19_[+2(1.64e-05)]_160_\ [+1(1.41e-07)]_236_[+3(4.16e-07)]_27 21045 1.13e-06 115_[+2(9.17e-07)]_145_\ [+3(1.46e-05)]_48_[+1(3.79e-06)]_134 22409 3.38e-05 118_[+3(4.64e-06)]_224_\ [+2(1.88e-05)]_52_[+1(2.67e-05)]_48 24364 1.37e-05 269_[+2(1.88e-05)]_31_\ [+3(6.37e-07)]_132_[+1(7.09e-05)]_10 24389 1.45e-09 235_[+2(2.38e-06)]_24_\ [+1(2.31e-08)]_5_[+3(6.37e-07)]_178 25695 2.80e-03 14_[+2(2.00e-05)]_357_\ [+1(1.24e-05)]_92 263836 3.24e-07 69_[+3(3.65e-06)]_20_[+2(2.38e-07)]_\ 124_[+1(1.46e-05)]_229 264759 3.24e-07 69_[+3(3.65e-06)]_20_[+2(2.38e-07)]_\ 124_[+1(1.46e-05)]_229 269573 5.44e-06 47_[+3(9.75e-06)]_111_\ [+1(3.30e-05)]_30_[+2(9.17e-07)]_254 32944 3.31e-03 302_[+1(1.71e-05)]_107_\ [+3(2.13e-05)]_54 41583 1.50e-05 108_[+2(1.52e-08)]_36_\ [+1(3.53e-05)]_319 6605 1.37e-07 140_[+2(4.51e-06)]_6_[+1(1.26e-06)]_\ 289_[+3(8.64e-07)]_7 8409 4.52e-05 151_[+1(2.78e-06)]_225_\ [+3(6.37e-07)]_47_[+3(1.89e-05)]_19 8880 1.60e-12 [+3(1.64e-07)]_204_[+1(2.04e-07)]_\ 180_[+2(7.14e-10)]_58 8999 4.55e-05 115_[+1(8.86e-06)]_160_\ [+2(1.54e-05)]_125_[+3(2.41e-05)]_42 9218 1.93e-07 174_[+2(9.17e-07)]_19_\ [+1(5.10e-06)]_100_[+3(1.54e-06)]_41_[+3(8.02e-05)]_87 9262 8.76e-15 18_[+2(1.94e-07)]_183_\ [+1(5.08e-08)]_155_[+3(4.45e-05)]_35_[+3(9.92e-12)]_30 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************