******************************************************************************** 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/62/62.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31544 1.0000 500 8940 1.0000 500 42934 1.0000 500 9137 1.0000 500 43140 1.0000 500 13476 1.0000 500 46706 1.0000 500 46720 1.0000 500 46729 1.0000 500 13253 1.0000 500 51040 1.0000 500 14307 1.0000 500 47746 1.0000 500 47762 1.0000 500 47925 1.0000 500 48133 1.0000 500 48204 1.0000 500 48449 1.0000 500 15089 1.0000 500 228 1.0000 500 29887 1.0000 500 43550 1.0000 500 43598 1.0000 500 43772 1.0000 500 48959 1.0000 500 49014 1.0000 500 8113 1.0000 500 16130 1.0000 500 49707 1.0000 500 40783 1.0000 500 51608 1.0000 500 44118 1.0000 500 50498 1.0000 500 44306 1.0000 500 33738 1.0000 500 44362 1.0000 500 44398 1.0000 500 26077 1.0000 500 34060 1.0000 500 44622 1.0000 500 44679 1.0000 500 11236 1.0000 500 45125 1.0000 500 45348 1.0000 500 12172 1.0000 500 45431 1.0000 500 20124 1.0000 500 45830 1.0000 500 36084 1.0000 500 54536 1.0000 500 42701 1.0000 500 46881 1.0000 500 48745 1.0000 500 43057 1.0000 500 46518 1.0000 500 50054 1.0000 500 47868 1.0000 500 49774 1.0000 500 45332 1.0000 500 46084 1.0000 500 45373 1.0000 500 44510 1.0000 500 48791 1.0000 500 35516 1.0000 500 50200 1.0000 500 40979 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/62/62.seqs.fa -oc motifs/62 -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= 66 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= 33000 N= 66 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.235 G 0.233 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.235 G 0.233 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 36 llr = 376 E-value = 2.3e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4361:19:6::1a83 pos.-specific C :414:31a::13:13 probability G 12:3:6:::a:6:1: matrix T 4132a:::4:9::14 bits 2.1 * 1.9 * * * 1.7 * * * * 1.5 * ** * * Relative 1.3 * ** ** * Entropy 1.1 * ***** * (15.1 bits) 0.8 * ***** ** 0.6 * ********** 0.4 * * ********** 0.2 *************** 0.0 --------------- Multilevel ACACTGACAGTGAAT consensus TATG C T C C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 26077 437 4.72e-08 GTCGTCGGGG TCTCTGACAGTGAAT TCGAAAGACT 50498 367 8.53e-08 TGCCCTTGAG AATCTGACAGTGAAT CTCACTGTAA 50200 56 2.24e-07 ACTATTCTAA GAACTGACAGTGAAC ACGGGGAATA 48791 321 2.74e-07 CAACCAGAAC TGACTGACTGTGAAA AATGCCCCTG 45348 281 2.74e-07 CCAAAACTAT TGATTGACAGTGAAT GATTTGCGGA 47925 359 2.74e-07 TCTTTTTTGA TATGTGACAGTGAAT CAACGTGGCT 43550 386 3.31e-07 ATCGACTAGA GCAGTGACAGTGAAT TACGACTCTA 9137 89 5.91e-07 TAGATACTGG TATCTCACTGTGAAT TCGATAGATT 46720 290 6.89e-07 GTTTCGGTTG ACCGTGACAGTGAAA CCAATCTCCC 44398 451 1.13e-06 TACTCGCTTA TCACTCACAGTAAAA TACCATTGGC 47762 221 2.52e-06 TTCTCTGTTA ATAGTCACAGTCAAC TAGACGAAAA 50054 290 4.22e-06 GCCCAATAAA AAACTGACACTGAAT AACACCCGAA 44306 381 5.62e-06 CTGTCACCAC ATCCTGACTGTCAAT ATCTTTGCCA 49707 236 5.62e-06 ACTCACTTTC ACAGTCACAGCCAAT CTCTACATTT 43598 371 6.19e-06 CTCCCTACAG AAACTAACAGTAAAC GGTGATACCA 42701 181 6.80e-06 AAATTGTGAA ACCATCACAGTCAAC TGCCAGGTGT 54536 341 6.80e-06 ATGAATGGAA AGATTGACAGTGATT GACAGTGATC 47746 443 6.80e-06 GCCACAACTG ACTGTGACAGTGACA ATGATGGACG 44510 287 8.14e-06 GAAATCTTCA TCGTTGACTGTGAAC GCGAACGAAC 15089 177 8.14e-06 CAAATCTCCA GCAATCACAGTCAAA CATTGGGTAG 46729 293 8.14e-06 TCGCCGGACG TGAATGACTGTGAGC TTTGTTTTCC 49774 423 8.91e-06 GTCGTACACA TATCTCACTGTCAGT GAGGTCGTTC 31544 292 9.73e-06 ACAACAGTCC TCACTGTCAGTCAAA GCGACCAATT 35516 379 1.06e-05 GCAACAAGCC AAACTAACTGTAAAC CCAAAATCTT 44362 343 1.06e-05 GCCGTGATTC ATTGTCACTGTCAAC CCCTTTTCTC 48133 357 1.06e-05 GTTTTCCGAA AACTTGACAGCGAAT CTTATTTCCA 45373 251 1.48e-05 GTAGGGCAAG AAACTGACAGGGAGC GAAGCGTATC 45830 210 1.48e-05 CGGGAGTCGT ACAGTTACAGTGAGT GCATCCATCG 20124 229 1.61e-05 TTATATATTT TCATTCACTGTTAAC ATAAACCAAT 48959 114 1.61e-05 TTTATCATGT GTATTCACAGTCAAA GGTTTTGGAT 43140 292 2.56e-05 GGATTTTCCC TGATTCCCTGTGAAA GGAAGTAGGG 48204 262 2.74e-05 CACGCTTCAT TCACTAACTGTAAGT AACTAGAAGT 48745 258 3.17e-05 CACAGCCAGT TCCCTGACAGCGACC TCGAATTGTA 42934 41 3.17e-05 TGCCGTTGGG AAAATGACTGTGCAA TGGGGATCCG 45125 294 3.40e-05 TGACAGCTTA TATCTGACAGTGATG GGTTCCATAT 44622 451 3.64e-05 CGCAAATCCG TGTGTCCCTGTGAAA GCGTATTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 26077 4.7e-08 436_[+1]_49 50498 8.5e-08 366_[+1]_119 50200 2.2e-07 55_[+1]_430 48791 2.7e-07 320_[+1]_165 45348 2.7e-07 280_[+1]_205 47925 2.7e-07 358_[+1]_127 43550 3.3e-07 385_[+1]_100 9137 5.9e-07 88_[+1]_397 46720 6.9e-07 289_[+1]_196 44398 1.1e-06 450_[+1]_35 47762 2.5e-06 220_[+1]_265 50054 4.2e-06 289_[+1]_196 44306 5.6e-06 380_[+1]_105 49707 5.6e-06 235_[+1]_250 43598 6.2e-06 370_[+1]_115 42701 6.8e-06 180_[+1]_305 54536 6.8e-06 340_[+1]_145 47746 6.8e-06 442_[+1]_43 44510 8.1e-06 286_[+1]_199 15089 8.1e-06 176_[+1]_309 46729 8.1e-06 292_[+1]_193 49774 8.9e-06 422_[+1]_63 31544 9.7e-06 291_[+1]_194 35516 1.1e-05 378_[+1]_107 44362 1.1e-05 342_[+1]_143 48133 1.1e-05 356_[+1]_129 45373 1.5e-05 250_[+1]_235 45830 1.5e-05 209_[+1]_276 20124 1.6e-05 228_[+1]_257 48959 1.6e-05 113_[+1]_372 43140 2.6e-05 291_[+1]_194 48204 2.7e-05 261_[+1]_224 48745 3.2e-05 257_[+1]_228 42934 3.2e-05 40_[+1]_445 45125 3.4e-05 293_[+1]_192 44622 3.6e-05 450_[+1]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=36 26077 ( 437) TCTCTGACAGTGAAT 1 50498 ( 367) AATCTGACAGTGAAT 1 50200 ( 56) GAACTGACAGTGAAC 1 48791 ( 321) TGACTGACTGTGAAA 1 45348 ( 281) TGATTGACAGTGAAT 1 47925 ( 359) TATGTGACAGTGAAT 1 43550 ( 386) GCAGTGACAGTGAAT 1 9137 ( 89) TATCTCACTGTGAAT 1 46720 ( 290) ACCGTGACAGTGAAA 1 44398 ( 451) TCACTCACAGTAAAA 1 47762 ( 221) ATAGTCACAGTCAAC 1 50054 ( 290) AAACTGACACTGAAT 1 44306 ( 381) ATCCTGACTGTCAAT 1 49707 ( 236) ACAGTCACAGCCAAT 1 43598 ( 371) AAACTAACAGTAAAC 1 42701 ( 181) ACCATCACAGTCAAC 1 54536 ( 341) AGATTGACAGTGATT 1 47746 ( 443) ACTGTGACAGTGACA 1 44510 ( 287) TCGTTGACTGTGAAC 1 15089 ( 177) GCAATCACAGTCAAA 1 46729 ( 293) TGAATGACTGTGAGC 1 49774 ( 423) TATCTCACTGTCAGT 1 31544 ( 292) TCACTGTCAGTCAAA 1 35516 ( 379) AAACTAACTGTAAAC 1 44362 ( 343) ATTGTCACTGTCAAC 1 48133 ( 357) AACTTGACAGCGAAT 1 45373 ( 251) AAACTGACAGGGAGC 1 45830 ( 210) ACAGTTACAGTGAGT 1 20124 ( 229) TCATTCACTGTTAAC 1 48959 ( 114) GTATTCACAGTCAAA 1 43140 ( 292) TGATTCCCTGTGAAA 1 48204 ( 262) TCACTAACTGTAAGT 1 48745 ( 258) TCCCTGACAGCGACC 1 42934 ( 41) AAAATGACTGTGCAA 1 45125 ( 294) TATCTGACAGTGATG 1 44622 ( 451) TGTGTCCCTGTGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 32076 bayes= 10.6464 E= 2.3e-015 74 -1181 -107 74 32 73 -48 -126 113 -76 -306 -9 -126 92 10 -45 -1181 -1181 -1181 191 -168 51 126 -326 178 -208 -1181 -326 -1181 209 -1181 -1181 126 -1181 -1181 44 -1181 -308 206 -1181 -1181 -149 -306 174 -126 9 139 -326 187 -308 -1181 -1181 149 -208 -74 -226 6 38 -306 55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 36 E= 2.3e-015 0.444444 0.000000 0.111111 0.444444 0.333333 0.388889 0.166667 0.111111 0.583333 0.138889 0.027778 0.250000 0.111111 0.444444 0.250000 0.194444 0.000000 0.000000 0.000000 1.000000 0.083333 0.333333 0.555556 0.027778 0.916667 0.055556 0.000000 0.027778 0.000000 1.000000 0.000000 0.000000 0.638889 0.000000 0.000000 0.361111 0.000000 0.027778 0.972222 0.000000 0.000000 0.083333 0.027778 0.888889 0.111111 0.250000 0.611111 0.027778 0.972222 0.027778 0.000000 0.000000 0.750000 0.055556 0.138889 0.055556 0.277778 0.305556 0.027778 0.388889 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][CA][AT][CG]T[GC]AC[AT]GT[GC]AA[TCA] -------------------------------------------------------------------------------- Time 31.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 39 llr = 383 E-value = 5.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 426334921668319319888 pos.-specific C 121243143:3144125::21 probability G 434423:262::23:4412:: matrix T 13:1:1:3:21113:11:::1 bits 2.1 1.9 1.7 1.5 * * * Relative 1.3 * * ** * Entropy 1.1 * * **** (14.2 bits) 0.8 * * ** * **** 0.6 * * **** * ***** 0.4 * * * * **** * ***** 0.2 * ***** ************* 0.0 --------------------- Multilevel AGAGCAACGAAACCAGCAAAA consensus GTGAAC TCGC AG AG G sequence A GG A T C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 12172 426 6.53e-10 CCTGGGGGAA GTAGACATGAAACCAGCAAAA CGACTCTATT 45332 368 2.16e-07 CGCCATCACG AAGGCAACGAAAAGCCCAAAA GCGGCTAACC 13476 254 3.36e-07 CAGCCCTGTG GGACGAAGGACACTACCAAAA GCACGAGTCG 46084 416 6.69e-07 CCCCAACTGG GGCTCAACCAAACGACCAAAA CCGTACCAAC 26077 49 8.70e-07 GTGTTGTGTG GGACAAAAGTAACTACGAAAA CACTTGTCGA 49707 362 8.70e-07 GATTCCATGT CAAGACACGAAAACAGGAACA AACTGTTTCA 20124 317 1.43e-06 GTAGAAAAGT ACATCGACCAAATCAAGAAAA TCCCATCTCG 50054 393 2.89e-06 TATCCGTGGA AAGTCCAACAAAACAACAACA GCAACACAAA 33738 94 2.89e-06 TGTATGGTCT GGAGCAATGTAGCGAGGAAAA AGGTAGCGGG 29887 280 2.89e-06 ATTGACGTTA AGGAGAACGAACCGAGGAACA ACCTCATGCA 43550 85 4.01e-06 AAGAGCAAAC ACAGCCATCGAAACATCAAAC GCGTGATCCC 36084 39 4.96e-06 GTACGTCGGC GAAGGAATGGAAGAAGGAGAA TTTTCCGAGG 8113 376 4.96e-06 ACCCTCATCG ATAGCGCCAACAACAACAAAA CGGACGTTGA 47762 391 4.96e-06 GGAATGTCAG AGACGGACCAAACCATCAGCA GGTTCACGCC 31544 392 4.96e-06 ATCAAACCTT TGGGAGATCTAACCAGCAACA GCTGAACGTC 48204 466 5.51e-06 TTTTGTTGAT TCGGATAGGACACCAGCAGAA ATCGATCTTT 44510 303 6.76e-06 ACTGTGAACG CGAACGAACACAATAGGAGAA AATCACAGAA 49774 322 7.48e-06 GCGCGACCGT GTGTGACAGACAGGAGCAAAA TGTCACGATG 49014 299 7.48e-06 GACAAGAACG ATGGACCTCACATCAGCAAAA TTCAGCCGAC 43140 103 8.26e-06 CGTGATCATA ATGAAAATATAAATAGGAAAA TGCTATCCAC 45348 256 1.10e-05 GTACTCGACG ACAAAGACGGACCAACCAAAA CTATTGATTG 16130 149 1.10e-05 TACGTGGGAG GAACAAAGCAAAACAACAGAC ATACACGAGT 47868 420 1.33e-05 CGATACAGAA AGGAAAAACGAACGCCCAGAA ACAGAGTATG 43057 108 1.33e-05 ATGTATGACG ATGGCGATGACAACATGAAGA AAATAATTGG 54536 416 1.33e-05 GTGTGAAAAC ATACACAAGACACGAGCGAAC ACGCTCATAG 51040 72 1.33e-05 CAAGCGCGGT ATGACTACGGAAACACAAAAA CTTTTAACCC 228 321 1.60e-05 TGCTAGCCGT GCAAGCAACTCAGAAGCAAAA GCCCTTTCGA 44362 101 2.94e-05 GGGACTCTGA CTAACTACCACAGTAACAGAA AAGACCAGAC 44306 63 3.20e-05 TAAACTACCT TCCACAAAAAAACTAAGAAAA ACATTGACAA 44679 155 3.47e-05 TCCCATTGAT GAGCACACGATACTAAAAAAA TTGAGCTAGA 46518 60 3.76e-05 GGACTCGTAC GGAACCAGCAATATACGGAAA GCATTTCTCG 44622 173 3.76e-05 AGTTCCGGGT ATCGCACAGAAATGAACAGAA ACTGCTGATT 43598 201 3.76e-05 TGTGACAGTC GCAGGAAGGAAACGATTAAAT GTCAGGCACT 14307 399 4.08e-05 GGCCCTCTGC GCGGGAACGGCAGTCACGAAA GAGCCGGAAA 46706 23 4.77e-05 ATGGCTTCGC AAAGCGACGAAAGCAATAACT AACGTGGGAT 40979 324 5.57e-05 TGCTACTACC GAATCGATGATCCGAGCAACA CTCGTGACCG 48133 427 5.57e-05 GTAAACCTCC GGAAAAATGGATATATGAAAC ATTGCTCACT 48791 250 6.47e-05 GTAGTCTTAG TCAGCCAGGGATGCAGGGAAA CTCTATGTGC 46720 137 8.06e-05 ATCGAATCAA AAGGGGACGTCTCGCGGAGAA TAACCTATTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12172 6.5e-10 425_[+2]_54 45332 2.2e-07 367_[+2]_112 13476 3.4e-07 253_[+2]_226 46084 6.7e-07 415_[+2]_64 26077 8.7e-07 48_[+2]_431 49707 8.7e-07 361_[+2]_118 20124 1.4e-06 316_[+2]_163 50054 2.9e-06 392_[+2]_87 33738 2.9e-06 93_[+2]_386 29887 2.9e-06 279_[+2]_200 43550 4e-06 84_[+2]_395 36084 5e-06 38_[+2]_441 8113 5e-06 375_[+2]_104 47762 5e-06 390_[+2]_89 31544 5e-06 391_[+2]_88 48204 5.5e-06 465_[+2]_14 44510 6.8e-06 302_[+2]_177 49774 7.5e-06 321_[+2]_158 49014 7.5e-06 298_[+2]_181 43140 8.3e-06 102_[+2]_377 45348 1.1e-05 255_[+2]_224 16130 1.1e-05 148_[+2]_331 47868 1.3e-05 419_[+2]_60 43057 1.3e-05 107_[+2]_372 54536 1.3e-05 415_[+2]_64 51040 1.3e-05 71_[+2]_408 228 1.6e-05 320_[+2]_159 44362 2.9e-05 100_[+2]_379 44306 3.2e-05 62_[+2]_417 44679 3.5e-05 154_[+2]_325 46518 3.8e-05 59_[+2]_420 44622 3.8e-05 172_[+2]_307 43598 3.8e-05 200_[+2]_279 14307 4.1e-05 398_[+2]_81 46706 4.8e-05 22_[+2]_457 40979 5.6e-05 323_[+2]_156 48133 5.6e-05 426_[+2]_53 48791 6.5e-05 249_[+2]_230 46720 8.1e-05 136_[+2]_343 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=39 12172 ( 426) GTAGACATGAAACCAGCAAAA 1 45332 ( 368) AAGGCAACGAAAAGCCCAAAA 1 13476 ( 254) GGACGAAGGACACTACCAAAA 1 46084 ( 416) GGCTCAACCAAACGACCAAAA 1 26077 ( 49) GGACAAAAGTAACTACGAAAA 1 49707 ( 362) CAAGACACGAAAACAGGAACA 1 20124 ( 317) ACATCGACCAAATCAAGAAAA 1 50054 ( 393) AAGTCCAACAAAACAACAACA 1 33738 ( 94) GGAGCAATGTAGCGAGGAAAA 1 29887 ( 280) AGGAGAACGAACCGAGGAACA 1 43550 ( 85) ACAGCCATCGAAACATCAAAC 1 36084 ( 39) GAAGGAATGGAAGAAGGAGAA 1 8113 ( 376) ATAGCGCCAACAACAACAAAA 1 47762 ( 391) AGACGGACCAAACCATCAGCA 1 31544 ( 392) TGGGAGATCTAACCAGCAACA 1 48204 ( 466) TCGGATAGGACACCAGCAGAA 1 44510 ( 303) CGAACGAACACAATAGGAGAA 1 49774 ( 322) GTGTGACAGACAGGAGCAAAA 1 49014 ( 299) ATGGACCTCACATCAGCAAAA 1 43140 ( 103) ATGAAAATATAAATAGGAAAA 1 45348 ( 256) ACAAAGACGGACCAACCAAAA 1 16130 ( 149) GAACAAAGCAAAACAACAGAC 1 47868 ( 420) AGGAAAAACGAACGCCCAGAA 1 43057 ( 108) ATGGCGATGACAACATGAAGA 1 54536 ( 416) ATACACAAGACACGAGCGAAC 1 51040 ( 72) ATGACTACGGAAACACAAAAA 1 228 ( 321) GCAAGCAACTCAGAAGCAAAA 1 44362 ( 101) CTAACTACCACAGTAACAGAA 1 44306 ( 63) TCCACAAAAAAACTAAGAAAA 1 44679 ( 155) GAGCACACGATACTAAAAAAA 1 46518 ( 60) GGAACCAGCAATATACGGAAA 1 44622 ( 173) ATCGCACAGAAATGAACAGAA 1 43598 ( 201) GCAGGAAGGAAACGATTAAAT 1 14307 ( 399) GCGGGAACGGCAGTCACGAAA 1 46706 ( 23) AAAGCGACGAAAGCAATAACT 1 40979 ( 324) GAATCGATGATCCGAGCAACA 1 48133 ( 427) GGAAAAATGGATATATGAAAC 1 48791 ( 250) TCAGCCAGGGATGCAGGGAAA 1 46720 ( 137) AAGGGGACGTCTCGCGGAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 31680 bayes= 9.88799 E= 5.9e+001 71 -161 72 -137 -21 -2 28 -5 108 -161 63 -1193 8 -61 91 -105 32 89 -1 -1193 62 13 14 -179 175 -119 -1193 -1193 -21 61 -60 -5 -179 51 134 -1193 127 -1193 -18 -79 127 39 -1193 -237 158 -161 -318 -137 21 89 -37 -179 -179 71 28 -5 175 -119 -1193 -1193 -6 -19 82 -105 -238 120 63 -237 175 -1193 -118 -1193 153 -1193 -1 -1193 158 -39 -318 -1193 167 -119 -1193 -237 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 39 E= 5.9e+001 0.435897 0.076923 0.384615 0.102564 0.230769 0.230769 0.282051 0.256410 0.564103 0.076923 0.358974 0.000000 0.282051 0.153846 0.435897 0.128205 0.333333 0.435897 0.230769 0.000000 0.410256 0.256410 0.256410 0.076923 0.897436 0.102564 0.000000 0.000000 0.230769 0.358974 0.153846 0.256410 0.076923 0.333333 0.589744 0.000000 0.641026 0.000000 0.205128 0.153846 0.641026 0.307692 0.000000 0.051282 0.794872 0.076923 0.025641 0.102564 0.307692 0.435897 0.179487 0.076923 0.076923 0.384615 0.282051 0.256410 0.897436 0.102564 0.000000 0.000000 0.256410 0.205128 0.410256 0.128205 0.051282 0.538462 0.358974 0.051282 0.897436 0.000000 0.102564 0.000000 0.769231 0.000000 0.230769 0.000000 0.794872 0.179487 0.025641 0.000000 0.846154 0.102564 0.000000 0.051282 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][GTAC][AG][GA][CAG][ACG]A[CTA][GC][AG][AC]A[CA][CGT]A[GAC][CG]A[AG]AA -------------------------------------------------------------------------------- Time 62.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 18 llr = 192 E-value = 2.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:::::::::32 pos.-specific C :181111:a2:2 probability G 891:::11:864 matrix T :1199989::23 bits 2.1 * 1.9 * 1.7 * ** 1.5 * *** ** Relative 1.3 ****** *** Entropy 1.1 ********** (15.4 bits) 0.8 ********** 0.6 *********** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel GGCTTTTTCGGG consensus A CAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9137 327 5.05e-08 TGATTTTCGG GGCTTTTTCGGG GTTGAACGCC 42701 385 5.07e-07 AGCAACGAAC AGCTTTTTCGGG TTCGGCCATG 8940 98 7.56e-07 TATTTCACCA GGCTTTTTCGTT GTGAACATGC 43140 70 9.56e-07 ACTAGCTCTC GGCTTCTTCGGG GCAAAATATG 34060 208 1.71e-06 CCTACGTGAG GGCTTCTTCGGT AGCCAAGCCT 20124 53 2.27e-06 TTGAGAATTT GGCTTTGTCGAG GAAAAGTGCG 228 356 2.61e-06 TTTCGACGAC GGCTCTTTCGGC ATCAACGAGG 35516 429 3.58e-06 TTCGTCAAGA AGCTTTTTCCGT TTCTCAAGCG 43057 142 3.58e-06 TAATTGGAGA AGCTTTTTCGAA GCAGCAGCGA 13476 32 6.15e-06 CTCAATCCGT GCCTTTTTCGGC GGCTTCACGG 50054 474 8.00e-06 GGAGTGAGAA GGCCTTTTCGTG GATGAACGGT 12172 282 8.00e-06 CTTGGGCGCG GGCTTTGTCCAG ACCCTACACG 47925 26 8.00e-06 TTTTTTTTAA GGTTTTTTCGAA TGCTGAGGTC 45431 95 1.07e-05 TGGCTAGTGT GGTTTTTTCGTC GTGGCGGTGG 48133 7 1.25e-05 TAGGAC AGCTTTCTCGGT CATCCTTCCA 49774 235 1.36e-05 TGAGCAACGA GGCTCTTTCCAT CAACGCGAGC 14307 357 2.21e-05 GGTGGATCTC GTCTTTTTCCGA GGGGCCAAGG 44362 312 2.54e-05 TAGTAGGGTA GGGTTTTGCGGG GGGTGATGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9137 5.1e-08 326_[+3]_162 42701 5.1e-07 384_[+3]_104 8940 7.6e-07 97_[+3]_391 43140 9.6e-07 69_[+3]_419 34060 1.7e-06 207_[+3]_281 20124 2.3e-06 52_[+3]_436 228 2.6e-06 355_[+3]_133 35516 3.6e-06 428_[+3]_60 43057 3.6e-06 141_[+3]_347 13476 6.1e-06 31_[+3]_457 50054 8e-06 473_[+3]_15 12172 8e-06 281_[+3]_207 47925 8e-06 25_[+3]_463 45431 1.1e-05 94_[+3]_394 48133 1.3e-05 6_[+3]_482 49774 1.4e-05 234_[+3]_254 14307 2.2e-05 356_[+3]_132 44362 2.5e-05 311_[+3]_177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=18 9137 ( 327) GGCTTTTTCGGG 1 42701 ( 385) AGCTTTTTCGGG 1 8940 ( 98) GGCTTTTTCGTT 1 43140 ( 70) GGCTTCTTCGGG 1 34060 ( 208) GGCTTCTTCGGT 1 20124 ( 53) GGCTTTGTCGAG 1 228 ( 356) GGCTCTTTCGGC 1 35516 ( 429) AGCTTTTTCCGT 1 43057 ( 142) AGCTTTTTCGAA 1 13476 ( 32) GCCTTTTTCGGC 1 50054 ( 474) GGCCTTTTCGTG 1 12172 ( 282) GGCTTTGTCCAG 1 47925 ( 26) GGTTTTTTCGAA 1 45431 ( 95) GGTTTTTTCGTC 1 48133 ( 7) AGCTTTCTCGGT 1 49774 ( 235) GGCTCTTTCCAT 1 14307 ( 357) GTCTTTTTCCGA 1 44362 ( 312) GGGTTTTGCGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 32274 bayes= 10.9417 E= 2.6e+002 -26 -1081 174 -1081 -1081 -208 193 -226 -1081 183 -206 -126 -1081 -208 -1081 183 -1081 -108 -1081 174 -1081 -108 -1081 174 -1081 -208 -107 165 -1081 -1081 -206 183 -1081 209 -1081 -1081 -1081 -8 174 -1081 6 -1081 125 -67 -68 -49 74 6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 2.6e+002 0.222222 0.000000 0.777778 0.000000 0.000000 0.055556 0.888889 0.055556 0.000000 0.833333 0.055556 0.111111 0.000000 0.055556 0.000000 0.944444 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.055556 0.111111 0.833333 0.000000 0.000000 0.055556 0.944444 0.000000 1.000000 0.000000 0.000000 0.000000 0.222222 0.777778 0.000000 0.277778 0.000000 0.555556 0.166667 0.166667 0.166667 0.388889 0.277778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA]GCTTTTTC[GC][GA][GT] -------------------------------------------------------------------------------- Time 95.75 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31544 1.63e-04 291_[+1(9.73e-06)]_85_\ [+2(4.96e-06)]_88 8940 2.15e-03 97_[+3(7.56e-07)]_391 42934 1.09e-02 40_[+1(3.17e-05)]_445 9137 7.55e-07 88_[+1(5.91e-07)]_223_\ [+3(5.05e-08)]_162 43140 3.96e-06 69_[+3(9.56e-07)]_21_[+2(8.26e-06)]_\ 168_[+1(2.56e-05)]_194 13476 3.99e-05 31_[+3(6.15e-06)]_210_\ [+2(3.36e-07)]_226 46706 1.79e-01 22_[+2(4.77e-05)]_457 46720 3.03e-04 136_[+2(8.06e-05)]_132_\ [+1(6.89e-07)]_196 46729 5.03e-02 292_[+1(8.14e-06)]_193 13253 9.15e-01 500 51040 9.45e-02 71_[+2(1.33e-05)]_408 14307 6.57e-03 313_[+3(7.59e-05)]_31_\ [+3(2.21e-05)]_30_[+2(4.08e-05)]_81 47746 7.32e-03 442_[+1(6.80e-06)]_43 47762 3.22e-05 220_[+1(2.52e-06)]_155_\ [+2(4.96e-06)]_89 47925 3.61e-05 25_[+3(8.00e-06)]_321_\ [+1(2.74e-07)]_45_[+1(2.56e-05)]_67 48133 9.40e-05 6_[+3(1.25e-05)]_338_[+1(1.06e-05)]_\ 55_[+2(5.57e-05)]_28_[+1(9.34e-05)]_10 48204 1.63e-03 261_[+1(2.74e-05)]_189_\ [+2(5.51e-06)]_14 48449 4.07e-01 500 15089 1.54e-02 82_[+1(4.17e-05)]_79_[+1(8.14e-06)]_\ 309 228 4.80e-04 320_[+2(1.60e-05)]_14_\ [+3(2.61e-06)]_133 29887 9.63e-04 279_[+2(2.89e-06)]_86_\ [+3(6.53e-05)]_102 43550 2.35e-05 54_[+1(6.15e-05)]_15_[+2(4.01e-06)]_\ 280_[+1(3.31e-07)]_100 43598 1.67e-03 63_[+1(5.77e-05)]_122_\ [+2(3.76e-05)]_149_[+1(6.19e-06)]_115 43772 7.68e-01 500 48959 9.97e-02 113_[+1(1.61e-05)]_260_\ [+1(4.76e-05)]_97 49014 5.74e-02 298_[+2(7.48e-06)]_181 8113 1.75e-02 306_[+2(6.47e-05)]_48_\ [+2(4.96e-06)]_104 16130 5.96e-02 148_[+2(1.10e-05)]_331 49707 3.36e-05 235_[+1(5.62e-06)]_111_\ [+2(8.70e-07)]_3_[+1(3.40e-05)]_100 40783 2.47e-01 500 51608 9.31e-01 500 44118 1.49e-01 181_[+3(8.82e-05)]_307 50498 1.85e-04 366_[+1(8.53e-08)]_119 44306 1.70e-03 62_[+2(3.20e-05)]_297_\ [+1(5.62e-06)]_105 33738 1.75e-02 93_[+2(2.89e-06)]_386 44362 9.99e-05 100_[+2(2.94e-05)]_190_\ [+3(2.54e-05)]_19_[+1(1.06e-05)]_143 44398 5.81e-03 214_[+1(1.48e-05)]_221_\ [+1(1.13e-06)]_35 26077 7.99e-07 48_[+2(8.70e-07)]_145_\ [+1(6.54e-05)]_207_[+1(4.72e-08)]_49 34060 1.54e-02 207_[+3(1.71e-06)]_281 44622 9.17e-03 172_[+2(3.76e-05)]_257_\ [+1(3.64e-05)]_35 44679 1.66e-01 154_[+2(3.47e-05)]_325 11236 4.09e-01 500 45125 1.76e-02 45_[+3(9.24e-05)]_236_\ [+1(3.40e-05)]_192 45348 6.92e-05 72_[+2(9.29e-05)]_162_\ [+2(1.10e-05)]_4_[+1(2.74e-07)]_205 12172 2.52e-07 281_[+3(8.00e-06)]_132_\ [+2(6.53e-10)]_54 45431 3.15e-02 94_[+3(1.07e-05)]_394 20124 1.19e-06 52_[+3(2.27e-06)]_164_\ [+1(1.61e-05)]_73_[+2(1.43e-06)]_163 45830 1.28e-02 209_[+1(1.48e-05)]_276 36084 3.48e-02 38_[+2(4.96e-06)]_441 54536 2.72e-04 340_[+1(6.80e-06)]_60_\ [+2(1.33e-05)]_64 42701 4.92e-05 52_[+3(7.59e-05)]_116_\ [+1(6.80e-06)]_189_[+3(5.07e-07)]_104 46881 4.12e-01 500 48745 8.02e-02 257_[+1(3.17e-05)]_228 43057 2.97e-04 107_[+2(1.33e-05)]_13_\ [+3(3.58e-06)]_347 46518 8.05e-02 59_[+2(3.76e-05)]_420 50054 2.07e-06 289_[+1(4.22e-06)]_88_\ [+2(2.89e-06)]_60_[+3(8.00e-06)]_15 47868 3.82e-02 419_[+2(1.33e-05)]_60 49774 1.50e-05 234_[+3(1.36e-05)]_75_\ [+2(7.48e-06)]_80_[+1(8.91e-06)]_63 45332 2.08e-03 367_[+2(2.16e-07)]_112 46084 3.39e-03 415_[+2(6.69e-07)]_64 45373 1.40e-02 250_[+1(1.48e-05)]_235 44510 4.83e-04 286_[+1(8.14e-06)]_1_[+2(6.76e-06)]_\ 107_[+1(7.84e-05)]_55 48791 2.79e-04 249_[+2(6.47e-05)]_50_\ [+1(2.74e-07)]_165 35516 5.39e-04 378_[+1(1.06e-05)]_35_\ [+3(3.58e-06)]_60 50200 4.70e-04 55_[+1(2.24e-07)]_430 40979 1.25e-01 323_[+2(5.57e-05)]_156 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************