******************************************************************************** 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/246/246.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1079 1.0000 500 15285 1.0000 500 19059 1.0000 500 2021 1.0000 500 21891 1.0000 500 22009 1.0000 500 22716 1.0000 500 22741 1.0000 500 23074 1.0000 500 23404 1.0000 500 23469 1.0000 500 24665 1.0000 500 24772 1.0000 500 25420 1.0000 500 25510 1.0000 500 25613 1.0000 500 263702 1.0000 500 263721 1.0000 500 268049 1.0000 500 268346 1.0000 500 269121 1.0000 500 29818 1.0000 500 33759 1.0000 500 35248 1.0000 500 5574 1.0000 500 7332 1.0000 500 9525 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/246/246.seqs.fa -oc motifs/246 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.239 G 0.236 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.239 G 0.236 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 19 llr = 226 E-value = 8.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 171153:2:11121::14: pos.-specific C :121::12123:1:1111: probability G 9:481:93:64132391:7 matrix T :24147149238477:863 bits 2.1 1.9 1.7 * * * 1.5 * * * * Relative 1.2 * * * * * * * Entropy 1.0 * * ** * * * * (17.1 bits) 0.8 ** * ** * * ****** 0.6 ** **** * * ****** 0.4 ******* ** * ****** 0.2 ******************* 0.0 ------------------- Multilevel GAGGATGTTGGTTTTGTTG consensus T TA G CT GGG AT sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 268049 194 6.29e-11 CCTATCCACC GAGGTTGTTGGTTTTGTAG TGTGTGTGGC 23469 107 3.56e-09 GGTGGTGATA GTTGTTGTTGTTGTTGTTG TGTGTTGCGA 22716 191 3.56e-09 ATGAGTCGAT GATGATGCTGTTATTGTTG ATGAGTGTGC 21891 34 7.89e-08 GAGGTGAAAC GATATTGTTCGTGTTGTTG GTTGCTGATG 15285 291 1.11e-07 ATCTCTTCAA GAGGAAGTTCGTTTGGTAT TCCTAGACCA 25510 149 3.20e-07 GGAATCAGCA GCGGTAGTTCTTGGTGTTG GTGTATCGGT 22009 87 6.95e-07 GTGGTGTAGC GAGGTTGGTGGGTTGCTTG CGATTGCGAT 19059 24 1.43e-06 ACGAGATGAA AAGGATGCTGTTGTTGGAG AGGACATGAG 2021 194 1.70e-06 CTCTGTTAGC GTTGATGTTTCATGTGTAG CGTCAGCCCT 33759 324 1.85e-06 ATCAGTTCTC GAGGGAGTTGCTCATGTAG ATGACGGTGA 25420 35 1.85e-06 GGTTGAAGTT GAGGATGATAGTTGCGTTG AATCAAGTTG 5574 317 2.01e-06 GGAAGGAGCG GCCCATGGTGGTATTGTAG CACGCACGAC 24665 51 2.01e-06 GGATGTGAAC GATGATTGTGCTGATGTTT GTACATGCAT 7332 41 3.55e-06 TCTTTTGCCA AATGGAGGTCTTTTGGTAG AGTTAGGGAT 22741 414 7.01e-06 TCAAGTGTAA GTCTTTGCTGTTTTGGTTT GATGTTGAGC 25613 292 8.11e-06 GCAAGGATGA GACGATGATGCTGTTGCCT TCCTTCCACA 23404 82 1.07e-05 GAAACGACAT GATGTTGGCTATTGTGTTT GGTGGCGGTG 1079 178 1.61e-05 GCAAGGTGAC GAGGTACTTGGAATGGATG CAACAGTAAA 9525 319 1.96e-05 CGGTGACAAT GAAGATGATTCTATTCATG AAAATCAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268049 6.3e-11 193_[+1]_288 23469 3.6e-09 106_[+1]_375 22716 3.6e-09 190_[+1]_291 21891 7.9e-08 33_[+1]_448 15285 1.1e-07 290_[+1]_191 25510 3.2e-07 148_[+1]_333 22009 6.9e-07 86_[+1]_395 19059 1.4e-06 23_[+1]_458 2021 1.7e-06 193_[+1]_288 33759 1.8e-06 323_[+1]_158 25420 1.8e-06 34_[+1]_447 5574 2e-06 316_[+1]_165 24665 2e-06 50_[+1]_431 7332 3.5e-06 40_[+1]_441 22741 7e-06 413_[+1]_68 25613 8.1e-06 291_[+1]_190 23404 1.1e-05 81_[+1]_400 1079 1.6e-05 177_[+1]_304 9525 2e-05 318_[+1]_163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=19 268049 ( 194) GAGGTTGTTGGTTTTGTAG 1 23469 ( 107) GTTGTTGTTGTTGTTGTTG 1 22716 ( 191) GATGATGCTGTTATTGTTG 1 21891 ( 34) GATATTGTTCGTGTTGTTG 1 15285 ( 291) GAGGAAGTTCGTTTGGTAT 1 25510 ( 149) GCGGTAGTTCTTGGTGTTG 1 22009 ( 87) GAGGTTGGTGGGTTGCTTG 1 19059 ( 24) AAGGATGCTGTTGTTGGAG 1 2021 ( 194) GTTGATGTTTCATGTGTAG 1 33759 ( 324) GAGGGAGTTGCTCATGTAG 1 25420 ( 35) GAGGATGATAGTTGCGTTG 1 5574 ( 317) GCCCATGGTGGTATTGTAG 1 24665 ( 51) GATGATTGTGCTGATGTTT 1 7332 ( 41) AATGGAGGTCTTTTGGTAG 1 22741 ( 414) GTCTTTGCTGTTTTGGTTT 1 25613 ( 292) GACGATGATGCTGTTGCCT 1 23404 ( 82) GATGTTGGCTATTGTGTTT 1 1079 ( 178) GAGGTACTTGGAATGGATG 1 9525 ( 319) GAAGATGATTCTATTCATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 13014 bayes= 9.61282 E= 8.8e-006 -134 -1089 192 -1089 147 -118 -1089 -71 -234 -60 83 51 -234 -218 183 -229 83 -1089 -117 71 -2 -1089 -1089 151 -1089 -218 192 -229 -75 -60 16 71 -1089 -218 -1089 187 -234 -18 129 -71 -234 14 64 29 -134 -1089 -216 170 -34 -218 42 71 -134 -1089 -17 141 -1089 -218 16 141 -1089 -118 192 -1089 -134 -218 -216 161 47 -218 -1089 116 -1089 -1089 164 3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 19 E= 8.8e-006 0.105263 0.000000 0.894737 0.000000 0.736842 0.105263 0.000000 0.157895 0.052632 0.157895 0.421053 0.368421 0.052632 0.052632 0.842105 0.052632 0.473684 0.000000 0.105263 0.421053 0.263158 0.000000 0.000000 0.736842 0.000000 0.052632 0.894737 0.052632 0.157895 0.157895 0.263158 0.421053 0.000000 0.052632 0.000000 0.947368 0.052632 0.210526 0.578947 0.157895 0.052632 0.263158 0.368421 0.315789 0.105263 0.000000 0.052632 0.842105 0.210526 0.052632 0.315789 0.421053 0.105263 0.000000 0.210526 0.684211 0.000000 0.052632 0.263158 0.684211 0.000000 0.105263 0.894737 0.000000 0.105263 0.052632 0.052632 0.789474 0.368421 0.052632 0.000000 0.578947 0.000000 0.000000 0.736842 0.263158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GA[GT]G[AT][TA]G[TG]T[GC][GTC]T[TGA][TG][TG]GT[TA][GT] -------------------------------------------------------------------------------- Time 6.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 13 llr = 186 E-value = 3.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::731:82:75:652:53755 pos.-specific C 58258a2:a328424856:45 probability G 21:1::::::12::22::32: matrix T 41221::8::2::22::1::1 bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * * Relative 1.2 * ***** * * Entropy 1.0 * ****** ** ** * (20.7 bits) 0.8 ** ****** ** **** 0.6 *** ****** ** ****** 0.4 *** ****** *** ****** 0.2 ************** ****** 0.0 --------------------- Multilevel CCACCCATCAACAACCCCAAA consensus T A CC CCG AAGCC sequence T TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263702 459 1.71e-10 AACATCTACA TCACCCATCACCCACCACACA GCCTCTCTGT 9525 229 3.82e-10 CTATCACGAG TCACCCATCAACATGCACAAA ATTGTCGACA 29818 80 1.41e-08 TCATCCGTCA CCACCCATCATGATCCCCGAA GAACAAGTGC 22009 236 1.58e-08 GGTAACAATC CCAACCCTCAACCCCCCAACA CCGACAAGAA 2021 30 2.45e-08 CTCTCGTCCT CCTCCCATCACCATTCCAACA CCAACCCTTC 22716 12 5.52e-08 AGGTGATGGG CCACCCATCCACAAACATAGC TCACATACGC 24772 166 2.20e-07 AAGAGGCTCC GCAGCCATCACCACGCAAGAC AATAGATGCG 21891 442 2.20e-07 GCAAAGTCCT GCCACCAACAACAACCCCGGC TCTCCAGCAA 19059 433 3.72e-07 CAGCCAGACG CTTCCCATCCACAAGCCCAAT CCCATCTCCC 268346 358 4.59e-07 CGAAGACCTT CCAACCAACCAGCATGCCACC ACCGACGTAG 23074 141 4.59e-07 GAGCCAGAGA TGCACCATCATCCAACCCGAC GTCGCTCACC 25613 239 1.05e-06 CCTCCTCGCC TCATACCTCCTCCCCCACACA AGCGCAAGCA 269121 112 1.39e-06 ATAGATCTAA TCATTCATCAGCAATGAAAAC GCGAAACGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263702 1.7e-10 458_[+2]_21 9525 3.8e-10 228_[+2]_251 29818 1.4e-08 79_[+2]_400 22009 1.6e-08 235_[+2]_244 2021 2.5e-08 29_[+2]_450 22716 5.5e-08 11_[+2]_468 24772 2.2e-07 165_[+2]_314 21891 2.2e-07 441_[+2]_38 19059 3.7e-07 432_[+2]_47 268346 4.6e-07 357_[+2]_122 23074 4.6e-07 140_[+2]_339 25613 1e-06 238_[+2]_241 269121 1.4e-06 111_[+2]_368 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=13 263702 ( 459) TCACCCATCACCCACCACACA 1 9525 ( 229) TCACCCATCAACATGCACAAA 1 29818 ( 80) CCACCCATCATGATCCCCGAA 1 22009 ( 236) CCAACCCTCAACCCCCCAACA 1 2021 ( 30) CCTCCCATCACCATTCCAACA 1 22716 ( 12) CCACCCATCCACAAACATAGC 1 24772 ( 166) GCAGCCATCACCACGCAAGAC 1 21891 ( 442) GCCACCAACAACAACCCCGGC 1 19059 ( 433) CTTCCCATCCACAAGCCCAAT 1 268346 ( 358) CCAACCAACCAGCATGCCACC 1 23074 ( 141) TGCACCATCATCCAACCCGAC 1 25613 ( 239) TCATACCTCCTCCCCCACACA 1 269121 ( 112) TCATTCATCAGCAATGAAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.4909 E= 3.4e-003 -1035 95 -62 57 -1035 182 -162 -174 138 -64 -1035 -75 21 95 -162 -75 -179 182 -1035 -174 -1035 206 -1035 -1035 167 -64 -1035 -1035 -79 -1035 -1035 171 -1035 206 -1035 -1035 138 36 -1035 -1035 79 -5 -162 -16 -1035 182 -62 -1035 121 69 -1035 -1035 101 -5 -1035 -16 -79 69 -3 -16 -1035 182 -62 -1035 79 117 -1035 -1035 21 136 -1035 -174 138 -1035 38 -1035 79 69 -62 -1035 79 95 -1035 -174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 3.4e-003 0.000000 0.461538 0.153846 0.384615 0.000000 0.846154 0.076923 0.076923 0.692308 0.153846 0.000000 0.153846 0.307692 0.461538 0.076923 0.153846 0.076923 0.846154 0.000000 0.076923 0.000000 1.000000 0.000000 0.000000 0.846154 0.153846 0.000000 0.000000 0.153846 0.000000 0.000000 0.846154 0.000000 1.000000 0.000000 0.000000 0.692308 0.307692 0.000000 0.000000 0.461538 0.230769 0.076923 0.230769 0.000000 0.846154 0.153846 0.000000 0.615385 0.384615 0.000000 0.000000 0.538462 0.230769 0.000000 0.230769 0.153846 0.384615 0.230769 0.230769 0.000000 0.846154 0.153846 0.000000 0.461538 0.538462 0.000000 0.000000 0.307692 0.615385 0.000000 0.076923 0.692308 0.000000 0.307692 0.000000 0.461538 0.384615 0.153846 0.000000 0.461538 0.461538 0.000000 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]CA[CA]CCATC[AC][ACT]C[AC][ACT][CGT]C[CA][CA][AG][AC][AC] -------------------------------------------------------------------------------- Time 12.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 27 llr = 260 E-value = 3.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1::1117::7:32434447 pos.-specific C 2:7:143174:617422142 probability G 61:9:25::6:15::23:11 matrix T 373172123:33111314:: bits 2.1 1.9 1.7 * 1.5 * Relative 1.2 * * Entropy 1.0 ** * * (13.9 bits) 0.8 **** **** * 0.6 ***** ***** ** *** 0.4 ***** ********* *** 0.2 *************** **** 0.0 -------------------- Multilevel GTCGTCGACGACGCCAAAAA consensus T T GC TCTTA ATGTCC sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 22009 155 6.34e-10 TAGGGTGGTC GTCGTCGACGTCGCCGGTCA AGTGAGAAAG 19059 394 3.50e-07 GATAGCTGTT GTCGTGCATCACGCCTCCCA CCACATCATC 22716 466 5.28e-07 TGAAAAACGA GTCGTTGACCTCACACAACC ACTCTAACCT 7332 276 1.65e-06 CCATTCTGCC GTCGTGTACCACTCATCTAA CATTGAATAG 25613 424 1.65e-06 AGCAGACGTC CTCGTTGACGACGACAATAG CTCAACGTCG 263702 414 1.86e-06 ACTCTCGAGA GTCGCAGCCGACGCCCGTCA TCGTCAATAA 24772 62 2.63e-06 TCACGCTCCC GTCTTCCTCCACGCCAGTGA TGTGAAACTA 1079 437 3.30e-06 GGTGCAAGGT GGCGTCCACCATCCCTGTCC GTTCGGCTCT 263721 461 3.68e-06 TCAACTCTCT CTCGTCCACCACACTGCCAA GGTGCATACG 25510 200 5.64e-06 CTGTGTGACT GTCGACGACGACGATGATGC AAACAGTATC 268049 28 6.26e-06 GTGTTGATGT TTCGACGATGTTGCATGAAC ATGGGTGCTG 24665 352 6.93e-06 CCCTATTCAA TTGGTGAACGACGCCAAAAA AGACTTCTTG 9525 155 9.35e-06 CCATCGCCGG GGTGTTCACGACGATAATCA TGCACACAGC 22741 217 1.37e-05 GAAGAGATTG TACTTCTACCACGCAAGAAA AGCAGGTGGT 33759 93 1.65e-05 CTGTGGCGAG TTTGTACATGATGAAAATAA CAAGACAGAA 2021 339 1.65e-05 GATGTCTTTG TTCGTCGCCGACATACTACA CATCTGATAT 5574 190 2.16e-05 CTCACAAGTA GTTGTGCACGATGCCGTTGG GGAGAGAGAG 25420 97 2.16e-05 CTATCCATCC GTTGTGGTTGATACTGCACA CATATACCTT 29818 337 2.57e-05 CTGATAATGC CTCGTCGACAATCACCAAAA ACGGCACATC 23404 33 2.57e-05 CTGACCGTTG GACGTGTACCTGCCCTGAAA AGTGTAGACA 268346 409 3.04e-05 CGCCAGCACC CACGATGACCACCCAGAACC ATCTCTAATC 35248 408 4.22e-05 GCTTTACTGA CTTGTCCTTCAGGTCTAACA CTCATAATTT 23469 454 5.33e-05 TTCGTGTAGC GTCGCTGTTGATACAATACC CTCCACCGGC 23074 356 5.33e-05 GTTGTGGTCG TGTGCAGACGAGGCACAAAA GAGTGGCAAA 269121 13 7.75e-05 GTACGAGCCT GTCGCCGACCTGTGATGTAA CCTAAATGAA 15285 11 9.59e-05 ATATCGACCT GATGTTGTTGTCACAACTGA TACGTCTCTC 21891 416 1.85e-04 CATTATCCAT TTCGACAATGTCATCTGCAA AGTCCTGCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22009 6.3e-10 154_[+3]_326 19059 3.5e-07 393_[+3]_87 22716 5.3e-07 465_[+3]_15 7332 1.7e-06 275_[+3]_205 25613 1.7e-06 423_[+3]_57 263702 1.9e-06 413_[+3]_67 24772 2.6e-06 61_[+3]_419 1079 3.3e-06 436_[+3]_44 263721 3.7e-06 460_[+3]_20 25510 5.6e-06 199_[+3]_281 268049 6.3e-06 27_[+3]_453 24665 6.9e-06 351_[+3]_129 9525 9.4e-06 154_[+3]_326 22741 1.4e-05 216_[+3]_264 33759 1.6e-05 92_[+3]_388 2021 1.6e-05 338_[+3]_142 5574 2.2e-05 189_[+3]_291 25420 2.2e-05 96_[+3]_384 29818 2.6e-05 336_[+3]_144 23404 2.6e-05 32_[+3]_448 268346 3e-05 408_[+3]_72 35248 4.2e-05 407_[+3]_73 23469 5.3e-05 453_[+3]_27 23074 5.3e-05 355_[+3]_125 269121 7.7e-05 12_[+3]_468 15285 9.6e-05 10_[+3]_470 21891 0.00018 415_[+3]_65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=27 22009 ( 155) GTCGTCGACGTCGCCGGTCA 1 19059 ( 394) GTCGTGCATCACGCCTCCCA 1 22716 ( 466) GTCGTTGACCTCACACAACC 1 7332 ( 276) GTCGTGTACCACTCATCTAA 1 25613 ( 424) CTCGTTGACGACGACAATAG 1 263702 ( 414) GTCGCAGCCGACGCCCGTCA 1 24772 ( 62) GTCTTCCTCCACGCCAGTGA 1 1079 ( 437) GGCGTCCACCATCCCTGTCC 1 263721 ( 461) CTCGTCCACCACACTGCCAA 1 25510 ( 200) GTCGACGACGACGATGATGC 1 268049 ( 28) TTCGACGATGTTGCATGAAC 1 24665 ( 352) TTGGTGAACGACGCCAAAAA 1 9525 ( 155) GGTGTTCACGACGATAATCA 1 22741 ( 217) TACTTCTACCACGCAAGAAA 1 33759 ( 93) TTTGTACATGATGAAAATAA 1 2021 ( 339) TTCGTCGCCGACATACTACA 1 5574 ( 190) GTTGTGCACGATGCCGTTGG 1 25420 ( 97) GTTGTGGTTGATACTGCACA 1 29818 ( 337) CTCGTCGACAATCACCAAAA 1 23404 ( 33) GACGTGTACCTGCCCTGAAA 1 268346 ( 409) CACGATGACCACCCAGAACC 1 35248 ( 408) CTTGTCCTTCAGGTCTAACA 1 23469 ( 454) GTCGCTGTTGATACAATACC 1 23074 ( 356) TGTGCAGACGAGGCACAAAA 1 269121 ( 13) GTCGCCGACCTGTGATGTAA 1 15285 ( 11) GATGTTGTTGTCACAACTGA 1 21891 ( 416) TTCGACAATGTCATCTGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 12987 bayes= 8.90689 E= 3.7e+000 -1140 -37 123 1 -85 -1140 -109 152 -1140 156 -267 1 -1140 -1140 197 -180 -85 -69 -1140 145 -126 89 -9 -22 -185 31 113 -122 147 -169 -1140 -48 -1140 156 -1140 20 -284 77 123 -1140 147 -1140 -1140 1 -1140 131 -67 1 -4 -69 113 -180 -52 148 -267 -122 61 89 -1140 -80 15 -37 -9 20 48 -37 50 -122 74 -110 -1140 78 74 77 -67 -1140 140 -11 -167 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 27 E= 3.7e+000 0.000000 0.185185 0.555556 0.259259 0.148148 0.000000 0.111111 0.740741 0.000000 0.703704 0.037037 0.259259 0.000000 0.000000 0.925926 0.074074 0.148148 0.148148 0.000000 0.703704 0.111111 0.444444 0.222222 0.222222 0.074074 0.296296 0.518519 0.111111 0.740741 0.074074 0.000000 0.185185 0.000000 0.703704 0.000000 0.296296 0.037037 0.407407 0.555556 0.000000 0.740741 0.000000 0.000000 0.259259 0.000000 0.592593 0.148148 0.259259 0.259259 0.148148 0.518519 0.074074 0.185185 0.666667 0.037037 0.111111 0.407407 0.444444 0.000000 0.148148 0.296296 0.185185 0.222222 0.296296 0.370370 0.185185 0.333333 0.111111 0.444444 0.111111 0.000000 0.444444 0.444444 0.407407 0.148148 0.000000 0.703704 0.222222 0.074074 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT]T[CT]GT[CGT][GC]A[CT][GC][AT][CT][GA]C[CA][ATG][AG][AT][AC][AC] -------------------------------------------------------------------------------- Time 18.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1079 8.65e-04 177_[+1(1.61e-05)]_240_\ [+3(3.30e-06)]_44 15285 9.23e-05 10_[+3(9.59e-05)]_260_\ [+1(1.11e-07)]_191 19059 6.79e-09 23_[+1(1.43e-06)]_351_\ [+3(3.50e-07)]_19_[+2(3.72e-07)]_47 2021 2.25e-08 29_[+2(2.45e-08)]_143_\ [+1(1.70e-06)]_126_[+3(1.65e-05)]_142 21891 8.90e-08 33_[+1(7.89e-08)]_389_\ [+2(2.20e-07)]_38 22009 4.96e-13 86_[+1(6.95e-07)]_49_[+3(6.34e-10)]_\ 61_[+2(1.58e-08)]_244 22716 6.33e-12 11_[+2(5.52e-08)]_158_\ [+1(3.56e-09)]_15_[+1(1.84e-05)]_222_[+3(5.28e-07)]_15 22741 3.55e-04 216_[+3(1.37e-05)]_177_\ [+1(7.01e-06)]_68 23074 2.59e-04 140_[+2(4.59e-07)]_194_\ [+3(5.33e-05)]_125 23404 1.88e-03 32_[+3(2.57e-05)]_29_[+1(1.07e-05)]_\ 400 23469 1.97e-06 106_[+1(3.56e-09)]_328_\ [+3(5.33e-05)]_27 24665 5.10e-05 50_[+1(2.01e-06)]_96_[+1(6.42e-05)]_\ 167_[+3(6.93e-06)]_129 24772 3.40e-06 61_[+3(2.63e-06)]_84_[+2(2.20e-07)]_\ 314 25420 4.60e-04 34_[+1(1.85e-06)]_43_[+3(2.16e-05)]_\ 384 25510 2.47e-05 148_[+1(3.20e-07)]_32_\ [+3(5.64e-06)]_281 25613 3.54e-07 238_[+2(1.05e-06)]_32_\ [+1(8.11e-06)]_113_[+3(1.65e-06)]_57 263702 1.50e-08 413_[+3(1.86e-06)]_25_\ [+2(1.71e-10)]_21 263721 3.52e-03 460_[+3(3.68e-06)]_20 268049 2.40e-08 7_[+1(1.54e-07)]_1_[+3(6.26e-06)]_\ 146_[+1(6.29e-11)]_288 268346 2.98e-04 357_[+2(4.59e-07)]_30_\ [+3(3.04e-05)]_72 269121 5.77e-04 12_[+3(7.75e-05)]_79_[+2(1.39e-06)]_\ 368 29818 4.38e-06 79_[+2(1.41e-08)]_236_\ [+3(2.57e-05)]_8_[+2(2.71e-05)]_115 33759 5.66e-04 92_[+3(1.65e-05)]_211_\ [+1(1.85e-06)]_44_[+1(7.16e-05)]_95 35248 1.12e-01 407_[+3(4.22e-05)]_73 5574 1.96e-04 189_[+3(2.16e-05)]_107_\ [+1(2.01e-06)]_165 7332 1.12e-04 40_[+1(3.55e-06)]_216_\ [+3(1.65e-06)]_205 9525 2.74e-09 154_[+3(9.35e-06)]_54_\ [+2(3.82e-10)]_69_[+1(1.96e-05)]_163 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************