******************************************************************************** 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/417/417.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10465 1.0000 500 10539 1.0000 500 10542 1.0000 500 10740 1.0000 500 18624 1.0000 500 19289 1.0000 500 20186 1.0000 500 20837 1.0000 500 21076 1.0000 500 21312 1.0000 500 22251 1.0000 500 22731 1.0000 500 23295 1.0000 500 23449 1.0000 500 23623 1.0000 500 23642 1.0000 500 23692 1.0000 500 24704 1.0000 500 24923 1.0000 500 24999 1.0000 500 25122 1.0000 500 25123 1.0000 500 25306 1.0000 500 25330 1.0000 500 25909 1.0000 500 262433 1.0000 500 268143 1.0000 500 268351 1.0000 500 269238 1.0000 500 2711 1.0000 500 4919 1.0000 500 4972 1.0000 500 5424 1.0000 500 7989 1.0000 500 9958 1.0000 500 bd1806 1.0000 500 bd1934 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/417/417.seqs.fa -oc motifs/417 -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= 37 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= 18500 N= 37 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.234 G 0.237 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.234 G 0.237 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 30 llr = 281 E-value = 1.8e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5:99:96a7439 pos.-specific C 181:a13:325: probability G 12::::1::521 matrix T 3::1:::::::: bits 2.1 * 1.9 * 1.7 * * 1.5 * ** * Relative 1.3 ***** * * Entropy 1.0 ***** ** * (13.5 bits) 0.8 ***** ** * 0.6 ********* * 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel ACAACAAAAGCA consensus T C CAA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 10542 465 8.08e-08 ACAAATCTAC ACAACAAAAGCA ACAGCAGGCA 10539 465 8.08e-08 ACAAATCTAC ACAACAAAAGCA ACAGCAGGCA 20186 443 2.51e-07 CATCGTTCAT ACAACAAAAACA AAGCCAACGC 7989 485 1.62e-06 TCGCTTGAAT ACAACAAACACA CATA 9958 377 2.35e-06 TTTGCCCCAA TCAACACAAGAA CTCTAATTTT 24704 348 3.50e-06 TTGTCAATGC GCAACAAAAGAA GAGCTGGTCA 23623 462 3.95e-06 CCGACTGGCG GCAACAAAAGGA AAGGCCAAAT 4972 430 4.29e-06 GAACAAAACA CCAACAAAAGCA GAGATACACC 4919 255 6.24e-06 AATTAAACAC ACAACACAACGA TCCAAACGTG 23295 5 6.24e-06 GCGA GCAACAAAAAGA AAGAACTTAC 25306 89 1.04e-05 CGACGAGACG ACAACAGAACCA TTGTCACAAC 25122 20 1.15e-05 ATAGATAGGA AGAACACAAGGA GTTGTGATGC 262433 431 1.70e-05 CTGATGGCGA TGAACAAACACA AGAAGAGTCA 20837 485 2.01e-05 TATTTGCAAC ACATCACACGCA GAGA 21076 440 2.19e-05 GAAGAAGTTG CCAACACAACCA CCGGCCCATC 25909 480 2.40e-05 AGAGGTCAAT TCAACAAACACG TCGCAACAT 23449 473 2.40e-05 ACGCAATGCA TCCACACAAGAA GAATTTGATA 22251 421 2.40e-05 GCAGTCCAAT TCACCAAAAGCA AAGCGACGGC 10465 257 2.64e-05 AGGGGAGAGA AGAACAAAAGCG TTCGGCTCGA 23692 486 2.89e-05 CCAAAAGCAT TGAACAAACAAA CGA 24923 12 3.14e-05 GGCCGTGGTA ACATCAAACAAA TGGACTGACT 25123 127 4.29e-05 TCATGGGTAA ACAACACACAAG CATCACAACT 23642 27 4.29e-05 TTCTCGGTGT TGAACACAACGA CAGTCTGGCT 25330 131 5.37e-05 TCACTTCATA GAAACAAAAGCA AACAAAACCT 2711 235 6.23e-05 CCGAGAAAAT TCAACAAGAAGA GAGTGGTGAT 268143 310 6.23e-05 TATGATTTGA TCCACAGAAGAA CGCAGTATGG bd1806 4 6.73e-05 CCA ACAACCGAAGAA TACAGCTCCA bd1934 385 7.20e-05 TATCAAATGC ACAACACACACT CACAACGATT 21312 487 7.67e-05 CGCTCTCCCC ACAACCAACCAA GC 269238 410 1.60e-04 TCTCACTTCA TCCTCACAAAGA AACGTTCCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10542 8.1e-08 464_[+1]_24 10539 8.1e-08 464_[+1]_24 20186 2.5e-07 442_[+1]_46 7989 1.6e-06 484_[+1]_4 9958 2.4e-06 376_[+1]_112 24704 3.5e-06 347_[+1]_141 23623 3.9e-06 461_[+1]_27 4972 4.3e-06 429_[+1]_59 4919 6.2e-06 254_[+1]_234 23295 6.2e-06 4_[+1]_484 25306 1e-05 88_[+1]_400 25122 1.1e-05 19_[+1]_469 262433 1.7e-05 430_[+1]_58 20837 2e-05 484_[+1]_4 21076 2.2e-05 439_[+1]_49 25909 2.4e-05 479_[+1]_9 23449 2.4e-05 472_[+1]_16 22251 2.4e-05 420_[+1]_68 10465 2.6e-05 256_[+1]_232 23692 2.9e-05 485_[+1]_3 24923 3.1e-05 11_[+1]_477 25123 4.3e-05 126_[+1]_362 23642 4.3e-05 26_[+1]_462 25330 5.4e-05 130_[+1]_358 2711 6.2e-05 234_[+1]_254 268143 6.2e-05 309_[+1]_179 bd1806 6.7e-05 3_[+1]_485 bd1934 7.2e-05 384_[+1]_104 21312 7.7e-05 486_[+1]_2 269238 0.00016 409_[+1]_79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=30 10542 ( 465) ACAACAAAAGCA 1 10539 ( 465) ACAACAAAAGCA 1 20186 ( 443) ACAACAAAAACA 1 7989 ( 485) ACAACAAACACA 1 9958 ( 377) TCAACACAAGAA 1 24704 ( 348) GCAACAAAAGAA 1 23623 ( 462) GCAACAAAAGGA 1 4972 ( 430) CCAACAAAAGCA 1 4919 ( 255) ACAACACAACGA 1 23295 ( 5) GCAACAAAAAGA 1 25306 ( 89) ACAACAGAACCA 1 25122 ( 20) AGAACACAAGGA 1 262433 ( 431) TGAACAAACACA 1 20837 ( 485) ACATCACACGCA 1 21076 ( 440) CCAACACAACCA 1 25909 ( 480) TCAACAAACACG 1 23449 ( 473) TCCACACAAGAA 1 22251 ( 421) TCACCAAAAGCA 1 10465 ( 257) AGAACAAAAGCG 1 23692 ( 486) TGAACAAACAAA 1 24923 ( 12) ACATCAAACAAA 1 25123 ( 127) ACAACACACAAG 1 23642 ( 27) TGAACACAACGA 1 25330 ( 131) GAAACAAAAGCA 1 2711 ( 235) TCAACAAGAAGA 1 268143 ( 310) TCCACAGAAGAA 1 bd1806 ( 4) ACAACCGAAGAA 1 bd1934 ( 385) ACAACACACACT 1 21312 ( 487) ACAACCAACCAA 1 269238 ( 410) TCCTCACAAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18093 bayes= 9.90898 E= 1.8e-009 80 -181 -83 36 -301 177 -51 -1155 175 -123 -1155 -1155 169 -281 -1155 -138 -1155 209 -1155 -1155 180 -181 -1155 -1155 108 51 -125 -1155 185 -1155 -283 -1155 138 36 -1155 -1155 45 -49 98 -1155 16 99 -2 -1155 169 -1155 -125 -296 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 30 E= 1.8e-009 0.466667 0.066667 0.133333 0.333333 0.033333 0.800000 0.166667 0.000000 0.900000 0.100000 0.000000 0.000000 0.866667 0.033333 0.000000 0.100000 0.000000 1.000000 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 0.566667 0.333333 0.100000 0.000000 0.966667 0.000000 0.033333 0.000000 0.700000 0.300000 0.000000 0.000000 0.366667 0.166667 0.466667 0.000000 0.300000 0.466667 0.233333 0.000000 0.866667 0.000000 0.100000 0.033333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT]CAACA[AC]A[AC][GA][CAG]A -------------------------------------------------------------------------------- Time 11.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 28 llr = 260 E-value = 1.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 13a92:76:82: pos.-specific C 66::79339186 probability G 11:1:1:::2:4 matrix T 3:::1::11::: bits 2.1 1.9 * 1.7 * 1.5 ** * * * Relative 1.3 ** * * * Entropy 1.0 ** ** * * (13.4 bits) 0.8 ********** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCAACCAACACC consensus TA A CC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 10465 231 1.07e-07 TCGTCCACTT CCAACCAACACG GCGGAGGGGA 22251 447 3.66e-07 GACGGCAGCA CCAACCACCACG ACTGTTTGCT 20837 463 7.90e-07 CGAACCCGAA CAAACCACCACC TATTTGCAAC 10542 199 2.85e-06 TTCACAGAAG CCAAACACCACG AGATGGACCC 10539 201 2.85e-06 TCGAGAGAAG CCAAACACCACG AGATGGACCC 23692 438 3.97e-06 TCTAGCCCTC CCAACCAACCCG ACCGGCCGTG 23295 450 4.56e-06 ACGCTGGCTG TCAACCAACAAC GAACAAACGG 22731 155 5.63e-06 TTGTTACGTG CCAACGCACACC GACCCAACAA 20186 489 8.85e-06 CAATACATTA CAAAACCACACG 2711 192 1.11e-05 TACGTTGACA CCAAAGAACACC TTGCAAAGTA 24999 172 1.11e-05 GTACTATTGA CGAAACCACACC TTAGCACCGT 25123 257 1.22e-05 AAAGGTGGTG TAAACCAACGCG ATGGAGAGCT 25330 405 1.49e-05 CCCACACACT CAAACCAACACA CACCTGTCCA 19289 36 1.49e-05 CAACCAGGCT ACAACCCCCACC ACCAACAACA 4919 306 1.65e-05 ATCGAGCACC CAAAACAACAAC ACGATATCAC 21312 328 2.17e-05 CGGCGAAACT CAAACCAATGCC AATCAATGGA 5424 124 2.84e-05 ATTTCGATGA TAAACCATCACG CTATAATAGG 25909 43 3.12e-05 TTACCACGGG GCAACCAATACG GGCAAACTCT 23449 446 3.35e-05 AGTGGTGGTG GCAACCCACAAC CGTAAACGCA 4972 62 3.65e-05 AACTGGCAGG TCAACCAATGCG TCTTCCGCGT 18624 489 4.31e-05 AGATCATCAT CGAACCATCGCC 269238 484 5.04e-05 ACACTCCTTG TAAGCCCACACC CATCA 21076 469 5.04e-05 ATCCAATCAG TCAACTACCACC ACTAAATCAC 7989 388 5.48e-05 TGCTGTCCGC TGAATCCACACC ACTCTCTCTA 24923 240 6.32e-05 CAAGGTAATC ACAATCACCACG AAGCAGTGTG bd1934 418 9.11e-05 AGCGCCCCAG CCAGCCCCTACC CGGCACCCTC bd1806 480 1.11e-04 ATCCTTCATT CCAACGAACCAC AGAATCAAC 9958 271 1.35e-04 ATATCAACAA CGAATCAACGAC GAAACGCAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10465 1.1e-07 230_[+2]_258 22251 3.7e-07 446_[+2]_42 20837 7.9e-07 462_[+2]_26 10542 2.8e-06 198_[+2]_290 10539 2.8e-06 200_[+2]_288 23692 4e-06 437_[+2]_51 23295 4.6e-06 449_[+2]_39 22731 5.6e-06 154_[+2]_334 20186 8.8e-06 488_[+2] 2711 1.1e-05 191_[+2]_297 24999 1.1e-05 171_[+2]_317 25123 1.2e-05 256_[+2]_232 25330 1.5e-05 404_[+2]_84 19289 1.5e-05 35_[+2]_453 4919 1.7e-05 305_[+2]_183 21312 2.2e-05 327_[+2]_161 5424 2.8e-05 123_[+2]_365 25909 3.1e-05 42_[+2]_446 23449 3.4e-05 445_[+2]_43 4972 3.7e-05 61_[+2]_427 18624 4.3e-05 488_[+2] 269238 5e-05 483_[+2]_5 21076 5e-05 468_[+2]_20 7989 5.5e-05 387_[+2]_101 24923 6.3e-05 239_[+2]_249 bd1934 9.1e-05 417_[+2]_71 bd1806 0.00011 479_[+2]_9 9958 0.00013 270_[+2]_218 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=28 10465 ( 231) CCAACCAACACG 1 22251 ( 447) CCAACCACCACG 1 20837 ( 463) CAAACCACCACC 1 10542 ( 199) CCAAACACCACG 1 10539 ( 201) CCAAACACCACG 1 23692 ( 438) CCAACCAACCCG 1 23295 ( 450) TCAACCAACAAC 1 22731 ( 155) CCAACGCACACC 1 20186 ( 489) CAAAACCACACG 1 2711 ( 192) CCAAAGAACACC 1 24999 ( 172) CGAAACCACACC 1 25123 ( 257) TAAACCAACGCG 1 25330 ( 405) CAAACCAACACA 1 19289 ( 36) ACAACCCCCACC 1 4919 ( 306) CAAAACAACAAC 1 21312 ( 328) CAAACCAATGCC 1 5424 ( 124) TAAACCATCACG 1 25909 ( 43) GCAACCAATACG 1 23449 ( 446) GCAACCCACAAC 1 4972 ( 62) TCAACCAATGCG 1 18624 ( 489) CGAACCATCGCC 1 269238 ( 484) TAAGCCCACACC 1 21076 ( 469) TCAACTACCACC 1 7989 ( 388) TGAATCCACACC 1 24923 ( 240) ACAATCACCACG 1 bd1934 ( 418) CCAGCCCCTACC 1 bd1806 ( 480) CCAACGAACCAC 1 9958 ( 271) CGAATCAACGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18093 bayes= 9.94004 E= 1.3e-004 -191 137 -173 -6 9 129 -73 -1145 190 -1145 -1145 -1145 179 -1145 -173 -1145 -32 153 -1145 -128 -1145 187 -115 -286 141 29 -1145 -1145 126 29 -1145 -186 -1145 187 -1145 -86 148 -171 -41 -1145 -59 181 -1145 -1145 -291 129 73 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 28 E= 1.3e-004 0.071429 0.607143 0.071429 0.250000 0.285714 0.571429 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.928571 0.000000 0.071429 0.000000 0.214286 0.678571 0.000000 0.107143 0.000000 0.857143 0.107143 0.035714 0.714286 0.285714 0.000000 0.000000 0.642857 0.285714 0.000000 0.071429 0.000000 0.857143 0.000000 0.142857 0.750000 0.071429 0.178571 0.000000 0.178571 0.821429 0.000000 0.000000 0.035714 0.571429 0.392857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][CA]AA[CA]C[AC][AC]CAC[CG] -------------------------------------------------------------------------------- Time 22.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 21 llr = 213 E-value = 2.9e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5:4::3::2::2 pos.-specific C :71aa:272:a: probability G 5:::::::2::: matrix T :34::7733a:7 bits 2.1 ** * 1.9 ** ** 1.7 ** ** 1.5 ** ** Relative 1.3 ** ** Entropy 1.0 ** *** * ** (14.7 bits) 0.8 ** ***** *** 0.6 ** ***** *** 0.4 ** ***** *** 0.2 ******** *** 0.0 ------------ Multilevel ACTCCTTCTTCT consensus GTA ACTA A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24999 113 1.09e-07 CATATAACGA ACTCCTTCTTCT GTATCTACTA 20186 294 9.68e-07 AGGGGTCTTT GTTCCTTCTTCT TCCACTTCTT 268143 82 1.42e-06 TCGCTTGTGA GCTCCTCCTTCT CTTCTCTCTT 19289 463 4.53e-06 GATACTACAT GCACCATCATCT CATAACTCAT 10465 439 5.12e-06 ACTACTATCG ATACCTTCGTCT TCTCGCTCTG 268351 449 5.86e-06 CTCTACGGAA GTTCCATCTTCT TGTCAGGCAT 10740 127 5.86e-06 CGAGTTGGTG GCACCTTCGTCA TCGTGGGCGT 25123 183 7.01e-06 AAGCCAGGAA GTTCCTTTCTCT CTCAACCCCA 25909 220 8.94e-06 CGTGCTTCAC GCTCCTCTCTCT CGGTACTCAA 25330 426 8.94e-06 ACACCTGTCC ATTCCTTTATCT CCTTCCATCG 18624 1 1.05e-05 . GCACCATCTTCA GTTCCACCCG 24704 208 1.39e-05 TTCCGAGTTG ACACCTCTCTCT CTCTCATGGT 4919 159 1.53e-05 CTCTGACATC ACCCCTCCATCT TGTGTACCAT 21312 41 1.53e-05 GAGCGATTGT ATACCTTCCTCA TACAACTCAA 4972 447 1.72e-05 AAGCAGAGAT ACACCATCATCA CCGTCTTCGA 20837 95 1.80e-05 CCAACTGCGC ATTCCTCTTTCT GATGATAATA 269238 336 1.89e-05 CAACAGCCTC ACTCCTACTTCT TCCGCCTTGG 10542 314 2.62e-05 TTTAAATATT GCCCCATTGTCT TGCGTCTTCA 10539 319 2.62e-05 TTTCAATATT GCCCCATTGTCT TGCGTCTTCA bd1806 111 2.87e-05 ATTGAATAGT ACACCTTCATCG AGATTGGCTG bd1934 189 3.53e-05 TAAGGAAGGG ACGCCTTCCTCA TTCCCGCCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24999 1.1e-07 112_[+3]_376 20186 9.7e-07 293_[+3]_195 268143 1.4e-06 81_[+3]_407 19289 4.5e-06 462_[+3]_26 10465 5.1e-06 438_[+3]_50 268351 5.9e-06 448_[+3]_40 10740 5.9e-06 126_[+3]_362 25123 7e-06 182_[+3]_306 25909 8.9e-06 219_[+3]_269 25330 8.9e-06 425_[+3]_63 18624 1.1e-05 [+3]_488 24704 1.4e-05 207_[+3]_281 4919 1.5e-05 158_[+3]_330 21312 1.5e-05 40_[+3]_448 4972 1.7e-05 446_[+3]_42 20837 1.8e-05 94_[+3]_394 269238 1.9e-05 335_[+3]_153 10542 2.6e-05 313_[+3]_175 10539 2.6e-05 318_[+3]_170 bd1806 2.9e-05 110_[+3]_378 bd1934 3.5e-05 188_[+3]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=21 24999 ( 113) ACTCCTTCTTCT 1 20186 ( 294) GTTCCTTCTTCT 1 268143 ( 82) GCTCCTCCTTCT 1 19289 ( 463) GCACCATCATCT 1 10465 ( 439) ATACCTTCGTCT 1 268351 ( 449) GTTCCATCTTCT 1 10740 ( 127) GCACCTTCGTCA 1 25123 ( 183) GTTCCTTTCTCT 1 25909 ( 220) GCTCCTCTCTCT 1 25330 ( 426) ATTCCTTTATCT 1 18624 ( 1) GCACCATCTTCA 1 24704 ( 208) ACACCTCTCTCT 1 4919 ( 159) ACCCCTCCATCT 1 21312 ( 41) ATACCTTCCTCA 1 4972 ( 447) ACACCATCATCA 1 20837 ( 95) ATTCCTCTTTCT 1 269238 ( 336) ACTCCTACTTCT 1 10542 ( 314) GCCCCATTGTCT 1 10539 ( 319) GCCCCATTGTCT 1 bd1806 ( 111) ACACCTTCATCG 1 bd1934 ( 189) ACGCCTTCCTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18093 bayes= 10.0543 E= 2.9e-004 96 -1104 100 -1104 -1104 151 -1104 36 50 -71 -231 72 -1104 209 -1104 -1104 -1104 209 -1104 -1104 9 -1104 -1104 146 -249 2 -1104 146 -1104 151 -1104 36 -17 2 -32 36 -1104 -1104 -1104 194 -1104 209 -1104 -1104 -17 -1104 -231 146 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 21 E= 2.9e-004 0.523810 0.000000 0.476190 0.000000 0.000000 0.666667 0.000000 0.333333 0.380952 0.142857 0.047619 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.000000 0.714286 0.047619 0.238095 0.000000 0.714286 0.000000 0.666667 0.000000 0.333333 0.238095 0.238095 0.190476 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.238095 0.000000 0.047619 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][CT][TA]CC[TA][TC][CT][TAC]TC[TA] -------------------------------------------------------------------------------- Time 33.14 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10465 3.78e-07 230_[+2(1.07e-07)]_14_\ [+1(2.64e-05)]_170_[+3(5.12e-06)]_50 10539 1.71e-07 200_[+2(2.85e-06)]_106_\ [+3(2.62e-05)]_134_[+1(8.08e-08)]_24 10542 1.71e-07 198_[+2(2.85e-06)]_103_\ [+3(2.62e-05)]_139_[+1(8.08e-08)]_24 10740 3.14e-02 126_[+3(5.86e-06)]_362 18624 5.46e-03 [+3(1.05e-05)]_476_[+2(4.31e-05)] 19289 4.97e-04 35_[+2(1.49e-05)]_415_\ [+3(4.53e-06)]_26 20186 6.70e-08 293_[+3(9.68e-07)]_137_\ [+1(2.51e-07)]_34_[+2(8.85e-06)] 20837 5.52e-06 94_[+3(1.80e-05)]_356_\ [+2(7.90e-07)]_10_[+1(2.01e-05)]_4 21076 2.54e-03 439_[+1(2.19e-05)]_17_\ [+2(5.04e-05)]_20 21312 2.75e-04 1_[+3(3.81e-05)]_27_[+3(1.53e-05)]_\ 275_[+2(2.17e-05)]_147_[+1(7.67e-05)]_2 22251 1.18e-04 420_[+1(2.40e-05)]_14_\ [+2(3.66e-07)]_42 22731 1.83e-02 154_[+2(5.63e-06)]_334 23295 3.51e-04 4_[+1(6.24e-06)]_433_[+2(4.56e-06)]_\ 39 23449 6.65e-03 445_[+2(3.35e-05)]_15_\ [+1(2.40e-05)]_16 23623 1.61e-02 461_[+1(3.95e-06)]_27 23642 1.00e-01 26_[+1(4.29e-05)]_462 23692 8.96e-04 437_[+2(3.97e-06)]_36_\ [+1(2.89e-05)]_3 24704 7.11e-04 207_[+3(1.39e-05)]_112_\ [+3(3.41e-05)]_4_[+1(3.50e-06)]_141 24923 5.57e-03 11_[+1(3.14e-05)]_216_\ [+2(6.32e-05)]_249 24999 2.84e-05 112_[+3(1.09e-07)]_47_\ [+2(1.11e-05)]_317 25122 4.85e-02 19_[+1(1.15e-05)]_469 25123 5.21e-05 126_[+1(4.29e-05)]_44_\ [+3(7.01e-06)]_62_[+2(1.22e-05)]_232 25306 1.24e-02 88_[+1(1.04e-05)]_400 25330 9.28e-05 130_[+1(5.37e-05)]_262_\ [+2(1.49e-05)]_9_[+3(8.94e-06)]_63 25909 8.79e-05 42_[+2(3.12e-05)]_165_\ [+3(8.94e-06)]_248_[+1(2.40e-05)]_9 262433 1.07e-01 430_[+1(1.70e-05)]_58 268143 1.36e-03 81_[+3(1.42e-06)]_216_\ [+1(6.23e-05)]_179 268351 1.64e-02 448_[+3(5.86e-06)]_40 269238 1.22e-03 335_[+3(1.89e-05)]_136_\ [+2(5.04e-05)]_5 2711 6.63e-03 191_[+2(1.11e-05)]_31_\ [+1(6.23e-05)]_254 4919 2.50e-05 158_[+3(1.53e-05)]_84_\ [+1(6.24e-06)]_39_[+2(1.65e-05)]_183 4972 3.48e-05 61_[+2(3.65e-05)]_356_\ [+1(4.29e-06)]_5_[+3(1.72e-05)]_42 5424 1.36e-01 123_[+2(2.84e-05)]_365 7989 3.77e-05 394_[+3(2.87e-05)]_78_\ [+1(1.62e-06)]_4 9958 1.51e-03 376_[+1(2.35e-06)]_112 bd1806 1.63e-03 3_[+1(6.73e-05)]_95_[+3(2.87e-05)]_\ 378 bd1934 1.74e-03 188_[+3(3.53e-05)]_184_\ [+1(7.20e-05)]_21_[+2(9.11e-05)]_71 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************