******************************************************************************** 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/43/43.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1014 1.0000 500 10271 1.0000 500 11993 1.0000 500 13806 1.0000 500 18109 1.0000 500 18190 1.0000 500 20266 1.0000 500 20750 1.0000 500 21858 1.0000 500 22879 1.0000 500 2291 1.0000 500 23284 1.0000 500 24350 1.0000 500 25793 1.0000 500 25794 1.0000 500 261083 1.0000 500 262229 1.0000 500 267979 1.0000 500 268271 1.0000 500 269764 1.0000 500 269985 1.0000 500 270361 1.0000 500 3057 1.0000 500 30939 1.0000 500 33161 1.0000 500 33709 1.0000 500 35200 1.0000 500 36614 1.0000 500 37187 1.0000 500 38216 1.0000 500 38272 1.0000 500 40001 1.0000 500 511 1.0000 500 5656 1.0000 500 8015 1.0000 500 9049 1.0000 500 9976 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/43/43.seqs.fa -oc motifs/43 -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 0.258 C 0.232 G 0.246 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.232 G 0.246 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 35 llr = 368 E-value = 3.9e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :5166:33136:44452393 pos.-specific C 83624936552855627517 probability G 1111:11::::111:2:2:: matrix T 1111::313121:::111:: bits 2.1 1.9 1.7 * 1.5 * * Relative 1.3 * * ** Entropy 1.1 * * * * ** (15.2 bits) 0.8 * ** * * * * ** 0.6 * ** * ***** * ** 0.4 ****** ******** **** 0.2 ******************** 0.0 -------------------- Multilevel CACAACACCCACCCCACCAC consensus C C TATAC AAA A A sequence C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25794 298 1.74e-08 CTCTCGTTGG CACGACAACCACACAACAAC AACACCGCCT 36614 467 2.38e-08 CCCCCCAACT CACAACTACAACCAACCAAC TGCGTGCGGG 262229 452 3.75e-08 CCCCTGTTCG TCCACCTCACACCCCACCAC TCACCCTCCC 37187 480 8.84e-08 CTCGAGCAAC CCAAACCACAACCAAACAAC C 22879 419 1.01e-07 GCGTGTTTTG CTCACCTCCACCACAACCAA CCAAACAAAT 261083 250 2.52e-07 TGTCCGTGGG CAGAACACACACCACATCAC CTACCTCCTC 20750 96 2.86e-07 ACAACCATTT CACAAGCCCAACAACACGAA ACATATCATC 38216 473 3.23e-07 TCACAACCTA CTCAACAACAACTCCACCAC CAAACACG 5656 471 3.65e-07 ACAACACACA CGCACCTCCTCCCCCACAAC GCTTTCCACC 30939 387 3.65e-07 GACAACACTG CAACACTCCAACACACCAAC AAGCCATTCA 40001 396 4.64e-07 GATGCAACCA CACAACACCAACCACTCCTC TATTACCCTT 23284 37 8.27e-07 TCTACAGTAT CCCAACGCCAACCACGACAA CGGTACATAA 269764 410 1.03e-06 TTTCACAAGT CACAACACCAACAAAAAGCC GCTCGCTCTC 18109 360 1.29e-06 GTCAGAAACA CCCGACCCTCACCAACCTAC AACGGCAACG 3057 157 1.96e-06 GCACTTCCGA TACAACTCAGACAACACCAC ACAACACGCC 9976 416 2.18e-06 TCTTCCTCTT TCCGCCACCCTGCCCACCAC ATTGTACATT 511 424 2.41e-06 CTCCGTCCGT CACTCCCCCCTCCGCTCCAC ACATTCGTCT 11993 367 2.41e-06 CTCGTTGTCA CACAACACTACTACCACTAC ATTTATCTCA 270361 216 2.95e-06 CATCAGTTCT CACAACAACCTAACACCAAC AATCAACCAC 269985 269 2.95e-06 TATCTTTTGC CCCCCCCATCACACCGTGAC AAGAAACTGC 25793 389 2.95e-06 GGTCGAGCGA CCACCCAACAACAAAGCCAA AGCAACGCTC 9049 252 8.39e-06 GACTACTCGA CACAACAATCTCGGCAACAC AGTTCTCTAT 8015 420 8.39e-06 TTGTGTTTCT CACCACGTTCAGCCCACAAC ACACGGAGCG 33709 328 1.99e-05 TTCCCATCCA CTGCACCCTCCCCCAATGAC GACGTTTTTG 267979 270 2.75e-05 TGAAAACAAA GACGACACGAACAACAACAC GGCAGAAGAG 21858 14 2.75e-05 ACTTCAAATG CATCACTCTCCTCAATCCAC TTTCGCACGG 2291 463 2.98e-05 ACACGCACCG CCTTCCTCCCTCCTCTCCAC TCTCGATTCA 18190 417 2.98e-05 TGTTGGTCTC CCCACGTCACACCCCCCGCA TGGCAGTCTG 1014 287 3.22e-05 CGCTGAGCTT CAGACCAACCAGACCAGGAA GATGGCTTGC 38272 412 5.08e-05 TACATGCAAA TGCAACTCTTTCCCACACAC GCTCACCTTT 33161 478 5.08e-05 TGAGCTTGCT GTTACCCACCACACAATCAA ACA 10271 457 5.08e-05 CCACGATCTT CCAACCTCTCCCGACGAAAA GCTGTCAAGA 268271 315 7.30e-05 AGCTTCGGCG CAGACGCTCTCCAAAACGAC GAGGATGGTG 24350 228 1.35e-04 GACAATCCAA CCAAGCCAATTCACCGCCAA CTATTTATTC 35200 474 1.64e-04 TCCTTGCTCG CCTTCCTTTCAGCCAGCAAA GGCCAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25794 1.7e-08 297_[+1]_183 36614 2.4e-08 466_[+1]_14 262229 3.7e-08 451_[+1]_29 37187 8.8e-08 479_[+1]_1 22879 1e-07 418_[+1]_62 261083 2.5e-07 249_[+1]_231 20750 2.9e-07 95_[+1]_385 38216 3.2e-07 472_[+1]_8 5656 3.7e-07 470_[+1]_10 30939 3.7e-07 386_[+1]_94 40001 4.6e-07 395_[+1]_85 23284 8.3e-07 36_[+1]_444 269764 1e-06 409_[+1]_71 18109 1.3e-06 359_[+1]_121 3057 2e-06 156_[+1]_324 9976 2.2e-06 415_[+1]_65 511 2.4e-06 423_[+1]_57 11993 2.4e-06 366_[+1]_114 270361 3e-06 215_[+1]_265 269985 3e-06 268_[+1]_212 25793 3e-06 388_[+1]_92 9049 8.4e-06 251_[+1]_229 8015 8.4e-06 419_[+1]_61 33709 2e-05 327_[+1]_153 267979 2.7e-05 269_[+1]_211 21858 2.7e-05 13_[+1]_467 2291 3e-05 462_[+1]_18 18190 3e-05 416_[+1]_64 1014 3.2e-05 286_[+1]_194 38272 5.1e-05 411_[+1]_69 33161 5.1e-05 477_[+1]_3 10271 5.1e-05 456_[+1]_24 268271 7.3e-05 314_[+1]_166 24350 0.00013 227_[+1]_253 35200 0.00016 473_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=35 25794 ( 298) CACGACAACCACACAACAAC 1 36614 ( 467) CACAACTACAACCAACCAAC 1 262229 ( 452) TCCACCTCACACCCCACCAC 1 37187 ( 480) CCAAACCACAACCAAACAAC 1 22879 ( 419) CTCACCTCCACCACAACCAA 1 261083 ( 250) CAGAACACACACCACATCAC 1 20750 ( 96) CACAAGCCCAACAACACGAA 1 38216 ( 473) CTCAACAACAACTCCACCAC 1 5656 ( 471) CGCACCTCCTCCCCCACAAC 1 30939 ( 387) CAACACTCCAACACACCAAC 1 40001 ( 396) CACAACACCAACCACTCCTC 1 23284 ( 37) CCCAACGCCAACCACGACAA 1 269764 ( 410) CACAACACCAACAAAAAGCC 1 18109 ( 360) CCCGACCCTCACCAACCTAC 1 3057 ( 157) TACAACTCAGACAACACCAC 1 9976 ( 416) TCCGCCACCCTGCCCACCAC 1 511 ( 424) CACTCCCCCCTCCGCTCCAC 1 11993 ( 367) CACAACACTACTACCACTAC 1 270361 ( 216) CACAACAACCTAACACCAAC 1 269985 ( 269) CCCCCCCATCACACCGTGAC 1 25793 ( 389) CCACCCAACAACAAAGCCAA 1 9049 ( 252) CACAACAATCTCGGCAACAC 1 8015 ( 420) CACCACGTTCAGCCCACAAC 1 33709 ( 328) CTGCACCCTCCCCCAATGAC 1 267979 ( 270) GACGACACGAACAACAACAC 1 21858 ( 14) CATCACTCTCCTCAATCCAC 1 2291 ( 463) CCTTCCTCCCTCCTCTCCAC 1 18190 ( 417) CCCACGTCACACCCCCCGCA 1 1014 ( 287) CAGACCAACCAGACCAGGAA 1 38272 ( 412) TGCAACTCTTTCCCACACAC 1 33161 ( 478) GTTACCCACCACACAATCAA 1 10271 ( 457) CCAACCTCTCCCGACGAAAA 1 268271 ( 315) CAGACGCTCTCCAAAACGAC 1 24350 ( 228) CCAAGCCAATTCACCGCCAA 1 35200 ( 474) CCTTCCTTTCAGCCAGCAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 17797 bayes= 9.0899 E= 3.9e-018 -1177 183 -210 -121 91 56 -210 -121 -85 144 -110 -121 129 -44 -110 -162 115 78 -310 -1177 -1177 198 -152 -1177 41 15 -210 38 29 137 -1177 -162 -85 122 -310 11 41 115 -310 -121 122 -22 -1177 -40 -317 178 -110 -221 73 106 -210 -321 63 115 -210 -321 73 130 -1177 -1177 107 -44 -52 -121 -59 156 -310 -121 0 106 -30 -221 183 -202 -1177 -321 15 162 -1177 -1177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 35 E= 3.9e-018 0.000000 0.828571 0.057143 0.114286 0.485714 0.342857 0.057143 0.114286 0.142857 0.628571 0.114286 0.114286 0.628571 0.171429 0.114286 0.085714 0.571429 0.400000 0.028571 0.000000 0.000000 0.914286 0.085714 0.000000 0.342857 0.257143 0.057143 0.342857 0.314286 0.600000 0.000000 0.085714 0.142857 0.542857 0.028571 0.285714 0.342857 0.514286 0.028571 0.114286 0.600000 0.200000 0.000000 0.200000 0.028571 0.800000 0.114286 0.057143 0.428571 0.485714 0.057143 0.028571 0.400000 0.514286 0.057143 0.028571 0.428571 0.571429 0.000000 0.000000 0.542857 0.171429 0.171429 0.114286 0.171429 0.685714 0.028571 0.114286 0.257143 0.485714 0.200000 0.057143 0.914286 0.057143 0.000000 0.028571 0.285714 0.714286 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC]CA[AC]C[ATC][CA][CT][CA][ACT]C[CA][CA][CA]AC[CAG]A[CA] -------------------------------------------------------------------------------- Time 13.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 22 llr = 247 E-value = 5.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :91:a3254:71:434 pos.-specific C ::3::22::::2::1: probability G a:1a::55:a:3a225 matrix T :15::51:6:35:441 bits 2.1 * * * * 1.9 * ** * * 1.7 * ** * * 1.5 ** ** * * Relative 1.3 ** ** * * Entropy 1.1 ** ** *** * (16.2 bits) 0.8 ** ** **** * 0.6 ** ** **** * * 0.4 ** ** **** * * 0.2 ************** * 0.0 ---------------- Multilevel GATGATGATGATGATG consensus C AAGA TG TAA sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25793 153 3.53e-08 ATTTGGTGGC GATGATAATGATGTTG TGACGTTGGG 262229 99 6.16e-08 GATGATGCTG GATGAAGGAGATGATG TGAATGCGGC 35200 207 4.94e-07 ACGTGTGAAG GATGATCGTGAGGTGA AGCCGACACA 261083 92 5.71e-07 AGGGTGGGTT GATGATGAAGTTGGTA TTGATAAAGT 1014 256 6.59e-07 TGCCACATCT GACGATGAAGTTGTTG TAGTTCGCTG 37187 83 1.18e-06 CCAGTAGGAT GATGATGGAGAGGAAT TAGTTGACAT 5656 299 1.33e-06 CCATGAAAGA GATGATCAAGTTGGTG TTCATGCTGC 268271 335 1.51e-06 CCAAAACGAC GAGGATGGTGAGGACG TCGAAGAAGA 18190 111 1.72e-06 TAGAGCAAGA GATGATGATGTAGATA AGAAGAATAG 2291 118 1.92e-06 TGCAAAGTGC GATGATCATGTGGTGA TGGCTTTGTG 3057 269 2.97e-06 GGGCGGCGAC GACGACGATGACGACA TGAAACGTCG 36614 219 3.26e-06 CTACGATCTT GACGAAGGAGACGTCA AAGTGGCGTG 9976 202 3.94e-06 GGTGGTGGAG GACGAAAGAGAGGAGA TAGAGTTAGA 40001 373 3.94e-06 ACTTCCGCGA GATGACGATGACGGAT GCAACCACAC 24350 374 4.73e-06 TAAGGGGATT GAGGAGGGTGATGATG TTGGCTATGA 33161 403 6.08e-06 TCAGAAGGGC GAAGAACGAGAGGTAG GGCGGGCGGC 22879 79 6.59e-06 TTGATGTGTG GATGAAAGTGACGCAG ACGACGATGC 30939 332 7.11e-06 CTATCAGATG GAGGAATGTGATGTGA GGTCTGTCGT 267979 216 1.23e-05 TTCTGACGTA GACGACAATGCTGAAG GACAAGACGT 270361 58 1.38e-05 GGGTAGACGG GAAGAAAATGAAGGAG GGCGTGAGAC 38272 337 1.55e-05 GTTGAGGTAC GTTGATCGTGTTGTTT GTTTGTCTGT 20266 237 2.31e-05 CTTCGTTCCT GTCGACTATGATGGAA ATCCACGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25793 3.5e-08 152_[+2]_332 262229 6.2e-08 98_[+2]_386 35200 4.9e-07 206_[+2]_278 261083 5.7e-07 91_[+2]_393 1014 6.6e-07 255_[+2]_229 37187 1.2e-06 82_[+2]_402 5656 1.3e-06 298_[+2]_186 268271 1.5e-06 334_[+2]_150 18190 1.7e-06 110_[+2]_374 2291 1.9e-06 117_[+2]_367 3057 3e-06 268_[+2]_216 36614 3.3e-06 218_[+2]_266 9976 3.9e-06 201_[+2]_283 40001 3.9e-06 372_[+2]_112 24350 4.7e-06 373_[+2]_111 33161 6.1e-06 402_[+2]_82 22879 6.6e-06 78_[+2]_406 30939 7.1e-06 331_[+2]_153 267979 1.2e-05 215_[+2]_269 270361 1.4e-05 57_[+2]_427 38272 1.6e-05 336_[+2]_148 20266 2.3e-05 236_[+2]_248 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=22 25793 ( 153) GATGATAATGATGTTG 1 262229 ( 99) GATGAAGGAGATGATG 1 35200 ( 207) GATGATCGTGAGGTGA 1 261083 ( 92) GATGATGAAGTTGGTA 1 1014 ( 256) GACGATGAAGTTGTTG 1 37187 ( 83) GATGATGGAGAGGAAT 1 5656 ( 299) GATGATCAAGTTGGTG 1 268271 ( 335) GAGGATGGTGAGGACG 1 18190 ( 111) GATGATGATGTAGATA 1 2291 ( 118) GATGATCATGTGGTGA 1 3057 ( 269) GACGACGATGACGACA 1 36614 ( 219) GACGAAGGAGACGTCA 1 9976 ( 202) GACGAAAGAGAGGAGA 1 40001 ( 373) GATGACGATGACGGAT 1 24350 ( 374) GAGGAGGGTGATGATG 1 33161 ( 403) GAAGAACGAGAGGTAG 1 22879 ( 79) GATGAAAGTGACGCAG 1 30939 ( 332) GAGGAATGTGATGTGA 1 267979 ( 216) GACGACAATGCTGAAG 1 270361 ( 58) GAAGAAAATGAAGGAG 1 38272 ( 337) GTTGATCGTGTTGTTT 1 20266 ( 237) GTCGACTATGATGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 17945 bayes= 10.0256 E= 5.3e-009 -1110 -1110 202 -1110 182 -1110 -1110 -154 -150 23 -85 92 -1110 -1110 202 -1110 196 -1110 -1110 -1110 30 -35 -243 78 -18 -3 89 -154 96 -1110 102 -1110 50 -1110 -1110 127 -1110 -1110 202 -1110 140 -235 -1110 5 -150 -35 15 78 -1110 -1110 202 -1110 50 -235 -11 46 30 -77 -43 46 67 -1110 89 -95 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 22 E= 5.3e-009 0.000000 0.000000 1.000000 0.000000 0.909091 0.000000 0.000000 0.090909 0.090909 0.272727 0.136364 0.500000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.318182 0.181818 0.045455 0.454545 0.227273 0.227273 0.454545 0.090909 0.500000 0.000000 0.500000 0.000000 0.363636 0.000000 0.000000 0.636364 0.000000 0.000000 1.000000 0.000000 0.681818 0.045455 0.000000 0.272727 0.090909 0.181818 0.272727 0.454545 0.000000 0.000000 1.000000 0.000000 0.363636 0.045455 0.227273 0.363636 0.318182 0.136364 0.181818 0.363636 0.409091 0.000000 0.454545 0.136364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GA[TC]GA[TA][GAC][AG][TA]G[AT][TG]G[ATG][TA][GA] -------------------------------------------------------------------------------- Time 24.96 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 37 llr = 291 E-value = 2.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:::2::::::: pos.-specific C 3:141492:222 probability G 5:26:213115: matrix T 1a6:84:59638 bits 2.1 1.9 * 1.7 * * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * * * * * (11.4 bits) 0.8 * ** * * * 0.6 **** **** * 0.4 ***** ****** 0.2 ************ 0.0 ------------ Multilevel GTTGTTCTTTGT consensus C GC C G CTC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 8015 279 7.16e-08 CAAATCTAGG GTTGTCCTTTGT GAGATCTTGC 18190 60 1.53e-07 CGGATTCACA GTTGTTCTTTGT TGGTTGCTAG 35200 443 1.32e-06 CCTTGAACCC CTTGTCCTTTTT CATTTTTCGT 2291 378 2.54e-06 TCCTCCTTGT GTTGTCCCTTGT CATTTAGTTT 25794 95 4.60e-06 ATGGGGACAA GTTCTGCTTTTT ACTACTTTAT 33161 357 9.00e-06 TGTAGCTTTT GTGGTTCGTTTT GTGGTTGTGC 269985 417 9.00e-06 TCTGTTGTTT GTTCTTCTTTGC ATTGGCATTA 33709 18 1.46e-05 GTTCTTTCAA GTTGATCGTTGT TCCTTTGAGC 11993 347 1.46e-05 ACATCGTTTC GTGGTGCTTTCT CGTTGTCACA 10271 400 1.87e-05 GTCCAATATT TTTCTCCTTTGT AATACCTTTC 262229 232 2.16e-05 GTGACAAGAA GTTGTGCGTGGT AGTTGAATAT 1014 35 2.50e-05 CTAACTCCAT CTTCTCCCTTTT CTGATTCCAA 36614 36 4.00e-05 GTGCGAGGAG CTCGTGCTTTTT CGAGTGGCTG 20750 387 4.47e-05 GAGAGTTTGA GTGGTTCGTGGT GAGTGAGCCC 18109 466 4.47e-05 AACTTCTAGG ATTGTCCCTTGT GGGCCTTTGT 5656 405 6.84e-05 GCTTCCTGTT CTTGTCCTTTAT TAGAAAGAGA 38272 135 8.33e-05 GTGCGACTTC CTCGTGCCTTGT GCTAACTCAT 23284 214 9.16e-05 AAGAGTGGCC CTTCCTCGTTGT CTCCACGGGT 511 24 1.01e-04 AATCTCGACA GTTGCTCCTTTT GCTGCTAGAT 3057 366 1.01e-04 CTTGCAATCG CTTGCGCGTTTT GCAACTGCTC 40001 210 1.21e-04 TCCCAGTTGA TTTGTGCTTTCC CGCCAAACGA 30939 469 1.32e-04 CAACAATCCG CTTCACCTTTTC ACAAGTCTAT 268271 185 1.32e-04 GGTGCACGGA TTGGTTCTTCTT CCGGTACTTT 38216 243 1.44e-04 TAGTTGACTG CTTGTTCTGTCT CATTGCCTCG 9049 364 1.56e-04 TATCACTGGC GTTCTTCCTCTC GTCTACTCGA 20266 224 1.56e-04 AGGTAAAGGA CTGCTTCGTTCC TGTCGACTAT 9976 120 1.98e-04 GTAGTTTTTT GTTGTGAGTTGT GGTCTCTTGA 25793 19 2.14e-04 CTTTATTTCG GTGGATCTTCGC GCGTCGAGAA 21858 138 2.31e-04 TTTCTTGACG CTTCAGCGTCTT CTTGGCTACT 22879 116 2.49e-04 TCTACGAACA GTGCACCGTCTT CAACATGTTG 267979 54 2.67e-04 ACGTCAGTCC ATGGTTCTTCGC GGGCGAGTCT 270361 11 2.88e-04 TCGGTGTTGG CTTCTCGTTTGC TTGGTTTGGT 261083 417 2.88e-04 ACTATCATCG ATTCTTCGTCGC TCCTCTTTCT 269764 210 3.78e-04 TGTTTCAAAG GTGCACCTTGCT TTTGCTCCAC 37187 436 5.17e-04 TGGCCTGTAC GTCGTCCGGCGT CGTCGTCCTC 13806 261 8.54e-04 CTGACGAGGA TTTGTACTTGCT AGTATCGAAT 24350 21 9.45e-04 GCCTTCTCCT GTCGTCGTTGCT GCATATGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8015 7.2e-08 278_[+3]_210 18190 1.5e-07 59_[+3]_429 35200 1.3e-06 442_[+3]_46 2291 2.5e-06 377_[+3]_111 25794 4.6e-06 94_[+3]_394 33161 9e-06 356_[+3]_132 269985 9e-06 416_[+3]_72 33709 1.5e-05 17_[+3]_471 11993 1.5e-05 346_[+3]_142 10271 1.9e-05 399_[+3]_89 262229 2.2e-05 231_[+3]_257 1014 2.5e-05 34_[+3]_454 36614 4e-05 35_[+3]_453 20750 4.5e-05 386_[+3]_102 18109 4.5e-05 465_[+3]_23 5656 6.8e-05 404_[+3]_84 38272 8.3e-05 134_[+3]_354 23284 9.2e-05 213_[+3]_275 511 0.0001 23_[+3]_465 3057 0.0001 365_[+3]_123 40001 0.00012 209_[+3]_279 30939 0.00013 468_[+3]_20 268271 0.00013 184_[+3]_304 38216 0.00014 242_[+3]_246 9049 0.00016 363_[+3]_125 20266 0.00016 223_[+3]_265 9976 0.0002 119_[+3]_369 25793 0.00021 18_[+3]_470 21858 0.00023 137_[+3]_351 22879 0.00025 115_[+3]_373 267979 0.00027 53_[+3]_435 270361 0.00029 10_[+3]_478 261083 0.00029 416_[+3]_72 269764 0.00038 209_[+3]_279 37187 0.00052 435_[+3]_53 13806 0.00085 260_[+3]_228 24350 0.00095 20_[+3]_468 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=37 8015 ( 279) GTTGTCCTTTGT 1 18190 ( 60) GTTGTTCTTTGT 1 35200 ( 443) CTTGTCCTTTTT 1 2291 ( 378) GTTGTCCCTTGT 1 25794 ( 95) GTTCTGCTTTTT 1 33161 ( 357) GTGGTTCGTTTT 1 269985 ( 417) GTTCTTCTTTGC 1 33709 ( 18) GTTGATCGTTGT 1 11993 ( 347) GTGGTGCTTTCT 1 10271 ( 400) TTTCTCCTTTGT 1 262229 ( 232) GTTGTGCGTGGT 1 1014 ( 35) CTTCTCCCTTTT 1 36614 ( 36) CTCGTGCTTTTT 1 20750 ( 387) GTGGTTCGTGGT 1 18109 ( 466) ATTGTCCCTTGT 1 5656 ( 405) CTTGTCCTTTAT 1 38272 ( 135) CTCGTGCCTTGT 1 23284 ( 214) CTTCCTCGTTGT 1 511 ( 24) GTTGCTCCTTTT 1 3057 ( 366) CTTGCGCGTTTT 1 40001 ( 210) TTTGTGCTTTCC 1 30939 ( 469) CTTCACCTTTTC 1 268271 ( 185) TTGGTTCTTCTT 1 38216 ( 243) CTTGTTCTGTCT 1 9049 ( 364) GTTCTTCCTCTC 1 20266 ( 224) CTGCTTCGTTCC 1 9976 ( 120) GTTGTGAGTTGT 1 25793 ( 19) GTGGATCTTCGC 1 21858 ( 138) CTTCAGCGTCTT 1 22879 ( 116) GTGCACCGTCTT 1 267979 ( 54) ATGGTTCTTCGC 1 270361 ( 11) CTTCTCGTTTGC 1 261083 ( 417) ATTCTTCGTCGC 1 269764 ( 210) GTGCACCTTGCT 1 37187 ( 436) GTCGTCCGGCGT 1 13806 ( 261) TTTGTACTTGCT 1 24350 ( 21) GTCGTCGTTGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18093 bayes= 8.93074 E= 2.0e+000 -167 48 98 -129 -1185 -1185 -1185 192 -1185 -110 -1 130 -1185 60 140 -1185 -67 -152 -1185 152 -325 60 -1 52 -325 198 -218 -1185 -1185 -52 40 96 -1185 -1185 -218 184 -1185 -10 -86 130 -325 -30 90 30 -1185 7 -1185 152 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 37 E= 2.0e+000 0.081081 0.324324 0.486486 0.108108 0.000000 0.000000 0.000000 1.000000 0.000000 0.108108 0.243243 0.648649 0.000000 0.351351 0.648649 0.000000 0.162162 0.081081 0.000000 0.756757 0.027027 0.351351 0.243243 0.378378 0.027027 0.918919 0.054054 0.000000 0.000000 0.162162 0.324324 0.513514 0.000000 0.000000 0.054054 0.945946 0.000000 0.216216 0.135135 0.648649 0.027027 0.189189 0.459459 0.324324 0.000000 0.243243 0.000000 0.756757 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]T[TG][GC]T[TCG]C[TG]T[TC][GT][TC] -------------------------------------------------------------------------------- Time 36.60 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1014 9.33e-06 34_[+3(2.50e-05)]_209_\ [+2(6.59e-07)]_15_[+1(3.22e-05)]_194 10271 2.44e-03 399_[+3(1.87e-05)]_45_\ [+1(5.08e-05)]_24 11993 2.89e-04 346_[+3(1.46e-05)]_8_[+1(2.41e-06)]_\ 69_[+1(6.33e-05)]_25 13806 6.69e-01 500 18109 5.66e-04 359_[+1(1.29e-06)]_86_\ [+3(4.47e-05)]_23 18190 2.12e-07 59_[+3(1.53e-07)]_39_[+2(1.72e-06)]_\ 290_[+1(2.98e-05)]_64 20266 2.27e-02 236_[+2(2.31e-05)]_248 20750 5.10e-05 95_[+1(2.86e-07)]_271_\ [+3(4.47e-05)]_102 21858 1.58e-02 13_[+1(2.75e-05)]_467 22879 3.17e-06 78_[+2(6.59e-06)]_324_\ [+1(1.01e-07)]_62 2291 2.95e-06 117_[+2(1.92e-06)]_244_\ [+3(2.54e-06)]_73_[+1(2.98e-05)]_18 23284 5.94e-04 36_[+1(8.27e-07)]_31_[+1(5.08e-05)]_\ 20_[+1(4.06e-05)]_66_[+3(9.16e-05)]_35_[+1(7.30e-05)]_220 24350 3.16e-03 373_[+2(4.73e-06)]_111 25793 5.26e-07 152_[+2(3.53e-08)]_220_\ [+1(2.95e-06)]_92 25794 3.30e-06 94_[+3(4.60e-06)]_109_\ [+3(8.33e-05)]_19_[+3(7.59e-05)]_10_[+1(1.68e-05)]_9_[+1(1.74e-08)]_127_\ [+1(2.16e-05)]_36 261083 9.08e-07 91_[+2(5.71e-07)]_142_\ [+1(2.52e-07)]_231 262229 2.05e-09 65_[+2(1.23e-05)]_17_[+2(6.16e-08)]_\ 117_[+3(2.16e-05)]_208_[+1(3.75e-08)]_29 267979 7.59e-04 215_[+2(1.23e-05)]_38_\ [+1(2.75e-05)]_211 268271 1.64e-04 314_[+1(7.30e-05)]_[+2(1.51e-06)]_\ 110_[+2(8.02e-05)]_24 269764 3.36e-04 102_[+2(9.20e-05)]_291_\ [+1(1.03e-06)]_25_[+1(5.47e-05)]_26 269985 3.66e-04 61_[+1(3.22e-05)]_187_\ [+1(2.95e-06)]_128_[+3(9.00e-06)]_72 270361 1.34e-04 57_[+2(1.38e-05)]_142_\ [+1(2.95e-06)]_265 3057 1.01e-05 156_[+1(1.96e-06)]_92_\ [+2(2.97e-06)]_216 30939 6.21e-06 331_[+2(7.11e-06)]_39_\ [+1(3.65e-07)]_73_[+1(5.47e-05)]_1 33161 4.00e-05 356_[+3(9.00e-06)]_34_\ [+2(6.08e-06)]_59_[+1(5.08e-05)]_3 33709 1.84e-03 17_[+3(1.46e-05)]_298_\ [+1(1.99e-05)]_153 35200 2.19e-06 206_[+2(4.94e-07)]_220_\ [+3(1.32e-06)]_46 36614 9.10e-08 35_[+3(4.00e-05)]_101_\ [+2(1.55e-05)]_54_[+2(3.26e-06)]_232_[+1(2.38e-08)]_14 37187 1.09e-06 82_[+2(1.18e-06)]_381_\ [+1(8.84e-08)]_1 38216 1.89e-04 472_[+1(3.23e-07)]_8 38272 5.99e-04 134_[+3(8.33e-05)]_171_\ [+2(9.20e-05)]_3_[+2(1.55e-05)]_59_[+1(5.08e-05)]_69 40001 4.20e-06 372_[+2(3.94e-06)]_7_[+1(4.64e-07)]_\ 85 511 2.92e-03 423_[+1(2.41e-06)]_57 5656 7.79e-07 298_[+2(1.33e-06)]_90_\ [+3(6.84e-05)]_54_[+1(3.65e-07)]_10 8015 1.74e-05 278_[+3(7.16e-08)]_129_\ [+1(8.39e-06)]_61 9049 8.21e-03 86_[+1(6.33e-05)]_23_[+1(7.84e-05)]_\ 102_[+1(8.39e-06)]_229 9976 2.52e-05 201_[+2(3.94e-06)]_157_\ [+1(7.84e-05)]_21_[+1(2.18e-06)]_11_[+1(6.38e-06)]_34 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************