******************************************************************************** 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/46/46.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42527 1.0000 500 42595 1.0000 500 17495 1.0000 500 42834 1.0000 500 32173 1.0000 500 43271 1.0000 500 50961 1.0000 500 20755 1.0000 500 46737 1.0000 500 46742 1.0000 500 46959 1.0000 500 37212 1.0000 500 47431 1.0000 500 37749 1.0000 500 47578 1.0000 500 6606 1.0000 500 48157 1.0000 500 48601 1.0000 500 48763 1.0000 500 42245 1.0000 500 18064 1.0000 500 32851 1.0000 500 43649 1.0000 500 9896 1.0000 500 25495 1.0000 500 23292 1.0000 500 49552 1.0000 500 23375 1.0000 500 49776 1.0000 500 49782 1.0000 500 49860 1.0000 500 50075 1.0000 500 50212 1.0000 500 33371 1.0000 500 44159 1.0000 500 50511 1.0000 500 2793 1.0000 500 44745 1.0000 500 44758 1.0000 500 11733 1.0000 500 45364 1.0000 500 12668 1.0000 500 12881 1.0000 500 46245 1.0000 500 43496 1.0000 500 48470 1.0000 500 42891 1.0000 500 50430 1.0000 500 43070 1.0000 500 43213 1.0000 500 43751 1.0000 500 46878 1.0000 500 50288 1.0000 500 45891 1.0000 500 47101 1.0000 500 32822 1.0000 500 47322 1.0000 500 47649 1.0000 500 49250 1.0000 500 47677 1.0000 500 48259 1.0000 500 44973 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/46/46.seqs.fa -oc motifs/46 -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= 62 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= 31000 N= 62 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.234 G 0.223 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.234 G 0.223 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 44 llr = 412 E-value = 7.7e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 24:::a:5:::9 pos.-specific C 313:3:a:::3: probability G 331:6::19:6: matrix T 236a2::41a:1 bits 2.2 1.9 * * * 1.7 * * ** 1.5 * ** ** * Relative 1.3 * ** ** * Entropy 1.1 * ** ** * (13.5 bits) 0.9 * ** **** 0.6 ***** **** 0.4 ********** 0.2 *********** 0.0 ------------ Multilevel CATTGACAGTGA consensus GGC C T C sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43271 262 1.95e-07 GATGTTTCAG GATTGACAGTGA TAGATTTACT 44745 393 2.58e-07 GTGAGAAACA GATTGACTGTGA ACAGAGTTTT 46878 306 4.17e-07 GGCTCAAAGT GGTTGACAGTGA GACGACATCT 43070 376 4.17e-07 TGTCTGCGAT CGTTGACTGTGA CTATGAATTC 37749 315 5.34e-07 CGCATAAGAG GGTTGACTGTGA GATACCGATA 43649 145 7.96e-07 ACCTAAGTAG TATTGACAGTGA AGAGGATTTT 47649 396 1.05e-06 TTTTGATCTG GACTGACAGTGA TGTCAACATG 49782 162 1.17e-06 GGCACGGACT GACTGACTGTGA CGCACTGCAA 50212 129 1.56e-06 TTGGTTTGGT AATTGACAGTGA TACAAAAACT 49860 428 1.56e-06 TTCCTCGACT TGTTGACAGTGA GTTCTGTCGT 17495 4 1.99e-06 CAC GGCTGACAGTGA CCGTGACAGG 49552 228 2.29e-06 GGTAGATTGA CTCTGACAGTGA ATCGGAATTC 23292 346 2.29e-06 CGAACCATCA TTTTGACAGTGA ATGTGCGAGA 42834 255 3.35e-06 GCGGGACAGA AGTTGACTGTGA CAACCTTTTC 37212 120 6.19e-06 GTCGAAGGAT CATTCACAGTCA ACTCTTTTCT 42595 163 7.32e-06 CTTGTCTGCG GATTCACAGTCA AAACACAGAG 45364 349 1.06e-05 TCAGTGACAT CGTTCACTGTCA GATCCGCAAA 33371 66 1.06e-05 CGATCAAAAC TGTTGACGGTGA TCAAAGCCGT 25495 177 1.28e-05 TTCGGTGAGA AAGTGACTGTGA ATGGCATCAA 45891 426 1.43e-05 CAACATCTCG TCTTGACTGTGA GTATCGCACG 42891 417 1.43e-05 CTTCTCGTTT GACTCACAGTCA CGGTTGAAAC 48259 351 1.55e-05 ACTTTTCAAG GACTCACTGTCA GCAGCACAGG 47431 201 2.04e-05 CAATTATTTT CTCTCACAGTCA GTCAAAACCC 43751 294 2.21e-05 CTGTGGTATA TTTTCACTGTCA CACGCTTGTA 44758 99 2.21e-05 TGCTTTGTCC CATTGACATTGA CACGTTGTGC 49776 423 2.21e-05 ACCGAAATGC CCTTGACGGTGA TCGGAAGTGC 18064 280 2.60e-05 ATAACAATTA CGGTTACAGTGA TGTATACGTG 50961 477 2.60e-05 ACTGTAAAAT ATTTCACAGTCA GTTTCGTTCG 50511 478 2.79e-05 CTCATCACTT TCTTCACTGTGA CTCACTCAAT 32173 392 3.03e-05 AGCAATCGAC AACTCACTGTCA ACAAAAAAAC 6606 225 3.25e-05 CGTCGTTCCT CTGTTACTGTGA TCGGTTCAGA 46742 168 3.51e-05 CCAAATGACA CTTTGACTGTAA CCAACCCCTA 47677 204 5.79e-05 CGTTCAATTG CACTGCCAGTGA TATAGTAGCA 12881 95 5.79e-05 TACTTTTGAC CACTTACGGTCA GTCGATACGT 9896 120 5.79e-05 GGCAAAAATG GATTGATTGTGA GAATCCTCCA 43213 397 6.66e-05 CCAGACGGAC GGGTTACGGTGA CTGGACCGAA 48157 141 6.66e-05 TACTAAACTC CGGTGACTGTGT CGAAGTTAAT 50075 402 7.12e-05 GTTTAACGTG GATTTACAGTTA CTGACCTTCC 42245 436 8.81e-05 AAATCTAGGA CTGTGACTTTGA CGCGCCCATT 32851 392 1.38e-04 TAATAGTAGA CATTCTCAGTCA ACGAAATCAC 42527 196 1.74e-04 ATTAGCTATG TTCTTACAGTGT TTTGATTGAA 20755 407 2.05e-04 AGGATGGACG TTCTTACTGTAA AAGTTCGATC 46959 469 2.37e-04 TTGCTAGGCA AATTGACAGTTT CCTTCGTTTT 44973 464 3.25e-04 GGGGGCCAAA ATTTCACGTTCA TTGGTGCTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43271 2e-07 261_[+1]_227 44745 2.6e-07 392_[+1]_96 46878 4.2e-07 305_[+1]_183 43070 4.2e-07 375_[+1]_113 37749 5.3e-07 314_[+1]_174 43649 8e-07 144_[+1]_344 47649 1e-06 395_[+1]_93 49782 1.2e-06 161_[+1]_327 50212 1.6e-06 128_[+1]_360 49860 1.6e-06 427_[+1]_61 17495 2e-06 3_[+1]_485 49552 2.3e-06 227_[+1]_261 23292 2.3e-06 345_[+1]_143 42834 3.3e-06 254_[+1]_234 37212 6.2e-06 119_[+1]_369 42595 7.3e-06 162_[+1]_326 45364 1.1e-05 348_[+1]_140 33371 1.1e-05 65_[+1]_423 25495 1.3e-05 176_[+1]_312 45891 1.4e-05 425_[+1]_63 42891 1.4e-05 416_[+1]_72 48259 1.6e-05 350_[+1]_138 47431 2e-05 200_[+1]_288 43751 2.2e-05 293_[+1]_195 44758 2.2e-05 98_[+1]_390 49776 2.2e-05 422_[+1]_66 18064 2.6e-05 279_[+1]_209 50961 2.6e-05 476_[+1]_12 50511 2.8e-05 477_[+1]_11 32173 3e-05 391_[+1]_97 6606 3.2e-05 224_[+1]_264 46742 3.5e-05 167_[+1]_321 47677 5.8e-05 203_[+1]_285 12881 5.8e-05 94_[+1]_394 9896 5.8e-05 119_[+1]_369 43213 6.7e-05 396_[+1]_92 48157 6.7e-05 140_[+1]_348 50075 7.1e-05 401_[+1]_87 42245 8.8e-05 435_[+1]_53 32851 0.00014 391_[+1]_97 42527 0.00017 195_[+1]_293 20755 0.0002 406_[+1]_82 46959 0.00024 468_[+1]_20 44973 0.00033 463_[+1]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=44 43271 ( 262) GATTGACAGTGA 1 44745 ( 393) GATTGACTGTGA 1 46878 ( 306) GGTTGACAGTGA 1 43070 ( 376) CGTTGACTGTGA 1 37749 ( 315) GGTTGACTGTGA 1 43649 ( 145) TATTGACAGTGA 1 47649 ( 396) GACTGACAGTGA 1 49782 ( 162) GACTGACTGTGA 1 50212 ( 129) AATTGACAGTGA 1 49860 ( 428) TGTTGACAGTGA 1 17495 ( 4) GGCTGACAGTGA 1 49552 ( 228) CTCTGACAGTGA 1 23292 ( 346) TTTTGACAGTGA 1 42834 ( 255) AGTTGACTGTGA 1 37212 ( 120) CATTCACAGTCA 1 42595 ( 163) GATTCACAGTCA 1 45364 ( 349) CGTTCACTGTCA 1 33371 ( 66) TGTTGACGGTGA 1 25495 ( 177) AAGTGACTGTGA 1 45891 ( 426) TCTTGACTGTGA 1 42891 ( 417) GACTCACAGTCA 1 48259 ( 351) GACTCACTGTCA 1 47431 ( 201) CTCTCACAGTCA 1 43751 ( 294) TTTTCACTGTCA 1 44758 ( 99) CATTGACATTGA 1 49776 ( 423) CCTTGACGGTGA 1 18064 ( 280) CGGTTACAGTGA 1 50961 ( 477) ATTTCACAGTCA 1 50511 ( 478) TCTTCACTGTGA 1 32173 ( 392) AACTCACTGTCA 1 6606 ( 225) CTGTTACTGTGA 1 46742 ( 168) CTTTGACTGTAA 1 47677 ( 204) CACTGCCAGTGA 1 12881 ( 95) CACTTACGGTCA 1 9896 ( 120) GATTGATTGTGA 1 43213 ( 397) GGGTTACGGTGA 1 48157 ( 141) CGGTGACTGTGT 1 50075 ( 402) GATTTACAGTTA 1 42245 ( 436) CTGTGACTTTGA 1 32851 ( 392) CATTCTCAGTCA 1 42527 ( 196) TTCTTACAGTGT 1 20755 ( 407) TTCTTACTGTAA 1 46959 ( 469) AATTGACAGTTT 1 44973 ( 464) ATTTCACGTTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 30318 bayes= 10.4539 E= 7.7e-020 -78 54 41 -40 66 -178 17 -11 -1210 22 -71 113 -1210 -1210 -1210 189 -1210 22 135 -76 181 -336 -1210 -357 -1210 206 -1210 -357 81 -1210 -97 60 -1210 -1210 206 -199 -1210 -1210 -1210 189 -258 22 151 -257 177 -1210 -1210 -199 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 44 E= 7.7e-020 0.159091 0.340909 0.295455 0.204545 0.431818 0.068182 0.250000 0.250000 0.000000 0.272727 0.136364 0.590909 0.000000 0.000000 0.000000 1.000000 0.000000 0.272727 0.568182 0.159091 0.954545 0.022727 0.000000 0.022727 0.000000 0.977273 0.000000 0.022727 0.477273 0.000000 0.113636 0.409091 0.000000 0.000000 0.931818 0.068182 0.000000 0.000000 0.000000 1.000000 0.045455 0.272727 0.636364 0.045455 0.931818 0.000000 0.000000 0.068182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CGT][AGT][TC]T[GC]AC[AT]GT[GC]A -------------------------------------------------------------------------------- Time 29.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 14 llr = 178 E-value = 8.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::411::2a:357:4: pos.-specific C :5:7::28:911:75: probability G 1122:a:::1221::a matrix T 944:9:8:::42231: bits 2.2 * * 1.9 * * * 1.7 * ** * 1.5 * * ** * Relative 1.3 * ** *** * Entropy 1.1 * ******* * * (18.3 bits) 0.9 * ******* ** * 0.6 ** ******* **** 0.4 ********** **** 0.2 **************** 0.0 ---------------- Multilevel TCACTGTCACTAACCG consensus TTG CA AGTTA sequence G GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 48601 389 4.79e-10 GATTGATGCA TCTCTGTCACTAACCG TACCGATTTT 46245 425 4.16e-08 ATTGGAGAGC TCTCTGTAACTAACAG CGAATATACA 45891 381 4.79e-08 GATCTGACTT TCGCTGTCACAAATCG GAAAGTGAAG 37212 53 2.40e-07 TGCAATAGTG TCAGTGTCACCAACAG AAACATAAAC 49776 330 4.41e-07 GACGCCGTCC TCACTGTCACGTTTCG GGGGTCATTC 47578 424 5.84e-07 CCCCTCCGAG TTGCTGCCACTGATCG CCGAATCAAT 20755 324 6.42e-07 CGAAGTGTCA TCTGTGTCACGCACAG CGCGAATCTC 49250 146 7.62e-07 TGCTCAGATT GTACTGTCACGTACCG CGTTCCCACA 44758 200 7.62e-07 GGCGAGGTAC TGACTGTAACAAATCG TCAAGGGTAA 50212 414 9.03e-07 TTACTTTCGT TGAGTGTCACAATCAG AATACACTGT 50961 185 2.09e-06 ACTGATTCTT TTTATGTCACTGTCAG TATCTCATTG 17495 347 3.09e-06 CTGCTACTAT TTGCTGTCACTGGCTG CTGTTGTTCT 44159 368 3.28e-06 ATCGTTGTCA TTTCAGCAACTTACCG TCAAAAGTTA 50075 75 3.94e-06 GTTGGCTTGC TCACAGCCAGAAACAG TTTGAAGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48601 4.8e-10 388_[+2]_96 46245 4.2e-08 424_[+2]_60 45891 4.8e-08 380_[+2]_104 37212 2.4e-07 52_[+2]_432 49776 4.4e-07 329_[+2]_155 47578 5.8e-07 423_[+2]_61 20755 6.4e-07 323_[+2]_161 49250 7.6e-07 145_[+2]_339 44758 7.6e-07 199_[+2]_285 50212 9e-07 413_[+2]_71 50961 2.1e-06 184_[+2]_300 17495 3.1e-06 346_[+2]_138 44159 3.3e-06 367_[+2]_117 50075 3.9e-06 74_[+2]_410 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=14 48601 ( 389) TCTCTGTCACTAACCG 1 46245 ( 425) TCTCTGTAACTAACAG 1 45891 ( 381) TCGCTGTCACAAATCG 1 37212 ( 53) TCAGTGTCACCAACAG 1 49776 ( 330) TCACTGTCACGTTTCG 1 47578 ( 424) TTGCTGCCACTGATCG 1 20755 ( 324) TCTGTGTCACGCACAG 1 49250 ( 146) GTACTGTCACGTACCG 1 44758 ( 200) TGACTGTAACAAATCG 1 50212 ( 414) TGAGTGTCACAATCAG 1 50961 ( 185) TTTATGTCACTGTCAG 1 17495 ( 347) TTGCTGTCACTGGCTG 1 44159 ( 368) TTTCAGCAACTTACCG 1 50075 ( 75) TCACAGCCAGAAACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 30070 bayes= 11.674 E= 8.0e+001 -1045 -1045 -164 178 -1045 110 -64 40 65 -1045 -6 40 -193 161 -6 -1045 -93 -1045 -1045 166 -1045 -1045 217 -1045 -1045 -13 -1045 154 -35 175 -1045 -1045 187 -1045 -1045 -1045 -1045 199 -164 -1045 7 -171 -6 66 87 -171 -6 -34 139 -1045 -164 -34 -1045 161 -1045 8 65 110 -1045 -192 -1045 -1045 217 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 14 E= 8.0e+001 0.000000 0.000000 0.071429 0.928571 0.000000 0.500000 0.142857 0.357143 0.428571 0.000000 0.214286 0.357143 0.071429 0.714286 0.214286 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.214286 0.000000 0.785714 0.214286 0.785714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.928571 0.071429 0.000000 0.285714 0.071429 0.214286 0.428571 0.500000 0.071429 0.214286 0.214286 0.714286 0.000000 0.071429 0.214286 0.000000 0.714286 0.000000 0.285714 0.428571 0.500000 0.000000 0.071429 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CT][ATG][CG]TG[TC][CA]AC[TAG][AGT][AT][CT][CA]G -------------------------------------------------------------------------------- Time 58.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 147 E-value = 5.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :23::116:::2:932:491: pos.-specific C 1:77:21:112::::::2::1 probability G :7:391:283684178a1199 matrix T 91::1682162:6::::2::: bits 2.2 * 1.9 * 1.7 * * ** 1.5 * * ** Relative 1.3 * ** * * ** *** Entropy 1.1 * *** * ****** *** (23.6 bits) 0.9 ***** * * ****** *** 0.6 ***** * ********* *** 0.4 ***** *********** *** 0.2 ********************* 0.0 --------------------- Multilevel TGCCGTTAGTGGTAGGGAAGG consensus AAG C G GCAG AA C sequence T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46737 309 1.89e-10 GCTACAGGAG TACCGGTAGGGGTAGGGAAGG AGGGGATGGA 47578 154 3.19e-10 TCGTGAGGTT TGCCGATAGTTGTAGGGTAGG GTAGGATAGA 48157 84 6.72e-10 TGTGTTATGT TGCCGTTAGTGAGAGGGAAAG ATGTGGGTTT 44758 155 5.58e-09 GTTCTTGTCA TGCGTTTGGGTGTAGGGCAGG GCTGGGCAAG 32822 439 2.83e-08 TCATCCAGAG TAACGTTTTTCGGAAGGAAGG TCCTTCGAAA 49860 41 5.50e-08 TGTTTAGGGA TGAGGTCAGTGGGAAAGAAGC TTAGACTTCG 32173 215 6.33e-08 GACCACTATT TTACGTTAGGGGGGGGGGGGG AAGATTGGGG 25495 479 6.78e-08 CTTTGGTTAT TGCCGCTTCTGATAAAGCAGG G 17495 132 1.47e-07 TTCCGTCACG CGCGGCAGGCCGTAGGGTAGG TGTACTCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46737 1.9e-10 308_[+3]_171 47578 3.2e-10 153_[+3]_326 48157 6.7e-10 83_[+3]_396 44758 5.6e-09 154_[+3]_325 32822 2.8e-08 438_[+3]_41 49860 5.5e-08 40_[+3]_439 32173 6.3e-08 214_[+3]_265 25495 6.8e-08 478_[+3]_1 17495 1.5e-07 131_[+3]_348 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 46737 ( 309) TACCGGTAGGGGTAGGGAAGG 1 47578 ( 154) TGCCGATAGTTGTAGGGTAGG 1 48157 ( 84) TGCCGTTAGTGAGAGGGAAAG 1 44758 ( 155) TGCGTTTGGGTGTAGGGCAGG 1 32822 ( 439) TAACGTTTTTCGGAAGGAAGG 1 49860 ( 41) TGAGGTCAGTGGGAAAGAAGC 1 32173 ( 215) TTACGTTAGGGGGGGGGGGGG 1 25495 ( 479) TGCCGCTTCTGATAAAGCAGG 1 17495 ( 132) CGCGGCAGGCCGTAGGGTAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 29760 bayes= 12.5389 E= 5.7e+002 -982 -107 -982 172 -30 -982 158 -128 29 151 -982 -982 -982 151 58 -982 -982 -982 200 -128 -129 -7 -100 104 -129 -107 -982 152 102 -982 0 -28 -982 -107 180 -128 -982 -107 58 104 -982 -7 132 -28 -30 -982 180 -982 -982 -982 100 104 170 -982 -100 -982 29 -982 158 -982 -30 -982 180 -982 -982 -982 217 -982 70 -7 -100 -28 170 -982 -100 -982 -129 -982 200 -982 -982 -107 200 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 5.7e+002 0.000000 0.111111 0.000000 0.888889 0.222222 0.000000 0.666667 0.111111 0.333333 0.666667 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.888889 0.111111 0.111111 0.222222 0.111111 0.555556 0.111111 0.111111 0.000000 0.777778 0.555556 0.000000 0.222222 0.222222 0.000000 0.111111 0.777778 0.111111 0.000000 0.111111 0.333333 0.555556 0.000000 0.222222 0.555556 0.222222 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 0.444444 0.555556 0.888889 0.000000 0.111111 0.000000 0.333333 0.000000 0.666667 0.000000 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 1.000000 0.000000 0.444444 0.222222 0.111111 0.222222 0.888889 0.000000 0.111111 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.111111 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GA][CA][CG]G[TC]T[AGT]G[TG][GCT][GA][TG]A[GA][GA]G[ACT]AGG -------------------------------------------------------------------------------- Time 87.21 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42527 4.11e-01 500 42595 2.65e-02 162_[+1(7.32e-06)]_326 17495 2.97e-08 3_[+1(1.99e-06)]_116_[+3(1.47e-07)]_\ 194_[+2(3.09e-06)]_138 42834 1.40e-03 154_[+3(3.48e-05)]_79_\ [+1(3.35e-06)]_234 32173 1.24e-05 214_[+3(6.33e-08)]_156_\ [+1(3.03e-05)]_97 43271 4.63e-04 143_[+1(3.25e-05)]_106_\ [+1(1.95e-07)]_12_[+1(2.83e-06)]_203 50961 9.19e-04 184_[+2(2.09e-06)]_276_\ [+1(2.60e-05)]_12 20755 7.22e-04 323_[+2(6.42e-07)]_161 46737 2.48e-06 308_[+3(1.89e-10)]_171 46742 6.08e-03 167_[+1(3.51e-05)]_321 46959 5.48e-01 500 37212 2.39e-05 52_[+2(2.40e-07)]_51_[+1(6.19e-06)]_\ 369 47431 7.95e-03 200_[+1(2.04e-05)]_288 37749 2.53e-05 12_[+3(4.03e-05)]_281_\ [+1(5.34e-07)]_174 47578 1.17e-08 153_[+3(3.19e-10)]_249_\ [+2(5.84e-07)]_61 6606 5.70e-02 224_[+1(3.25e-05)]_264 48157 9.28e-07 83_[+3(6.72e-10)]_36_[+1(6.66e-05)]_\ 348 48601 8.55e-06 388_[+2(4.79e-10)]_96 48763 4.89e-01 500 42245 9.23e-02 435_[+1(8.81e-05)]_53 18064 3.62e-02 279_[+1(2.60e-05)]_209 32851 2.63e-01 500 43649 6.58e-03 144_[+1(7.96e-07)]_344 9896 1.65e-01 119_[+1(5.79e-05)]_369 25495 1.29e-05 176_[+1(1.28e-05)]_290_\ [+3(6.78e-08)]_1 23292 1.84e-02 345_[+1(2.29e-06)]_143 49552 4.56e-03 227_[+1(2.29e-06)]_261 23375 2.81e-01 500 49776 7.36e-05 26_[+2(6.98e-05)]_88_[+2(2.46e-05)]_\ 183_[+2(4.41e-07)]_77_[+1(2.21e-05)]_66 49782 1.38e-03 161_[+1(1.17e-06)]_327 49860 2.19e-06 40_[+3(5.50e-08)]_366_\ [+1(1.56e-06)]_61 50075 2.75e-03 74_[+2(3.94e-06)]_311_\ [+1(7.12e-05)]_87 50212 4.13e-05 128_[+1(1.56e-06)]_31_\ [+2(6.10e-06)]_226_[+2(9.03e-07)]_71 33371 2.23e-02 65_[+1(1.06e-05)]_423 44159 1.60e-02 367_[+2(3.28e-06)]_117 50511 7.19e-02 477_[+1(2.79e-05)]_11 2793 6.56e-01 500 44745 9.14e-05 24_[+3(6.29e-05)]_327_\ [+1(4.67e-05)]_8_[+1(2.58e-07)]_96 44758 3.66e-09 98_[+1(2.21e-05)]_44_[+3(5.58e-09)]_\ 24_[+2(7.62e-07)]_285 11733 5.19e-01 500 45364 3.55e-02 348_[+1(1.06e-05)]_58_\ [+1(6.66e-05)]_70 12668 3.34e-01 500 12881 1.05e-01 94_[+1(5.79e-05)]_394 46245 5.12e-04 424_[+2(4.16e-08)]_60 43496 2.14e-01 500 48470 4.31e-01 500 42891 5.73e-03 224_[+1(2.60e-05)]_180_\ [+1(1.43e-05)]_72 50430 7.90e-01 500 43070 1.32e-03 285_[+1(1.28e-05)]_78_\ [+1(4.17e-07)]_113 43213 2.17e-01 396_[+1(6.66e-05)]_92 43751 1.89e-02 117_[+1(4.97e-05)]_164_\ [+1(2.21e-05)]_195 46878 1.12e-03 305_[+1(4.17e-07)]_183 50288 9.08e-01 500 45891 2.04e-05 90_[+2(8.04e-05)]_274_\ [+2(4.79e-08)]_29_[+1(1.43e-05)]_63 47101 4.98e-01 500 32822 1.77e-04 438_[+3(2.83e-08)]_41 47322 4.70e-01 500 47649 1.87e-03 395_[+1(1.05e-06)]_93 49250 2.13e-03 145_[+2(7.62e-07)]_339 47677 1.86e-02 203_[+1(5.79e-05)]_285 48259 1.39e-02 350_[+1(1.55e-05)]_138 44973 5.43e-02 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************