******************************************************************************** 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/94/94.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10073 1.0000 500 1009 1.0000 500 10106 1.0000 500 10750 1.0000 500 11089 1.0000 500 11548 1.0000 500 1196 1.0000 500 1210 1.0000 500 1243 1.0000 500 1594 1.0000 500 1904 1.0000 500 1931 1.0000 500 20931 1.0000 500 21016 1.0000 500 22484 1.0000 500 23223 1.0000 500 23875 1.0000 500 24282 1.0000 500 24466 1.0000 500 261541 1.0000 500 263271 1.0000 500 263852 1.0000 500 31062 1.0000 500 3123 1.0000 500 3361 1.0000 500 37302 1.0000 500 39677 1.0000 500 4166 1.0000 500 4167 1.0000 500 4491 1.0000 500 4653 1.0000 500 5018 1.0000 500 5192 1.0000 500 5401 1.0000 500 6203 1.0000 500 6204 1.0000 500 6536 1.0000 500 6626 1.0000 500 7237 1.0000 500 7505 1.0000 500 8110 1.0000 500 8263 1.0000 500 8511 1.0000 500 9055 1.0000 500 9286 1.0000 500 bd622 1.0000 500 bd856 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/94/94.seqs.fa -oc motifs/94 -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= 47 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= 23500 N= 47 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.275 C 0.232 G 0.225 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.232 G 0.225 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 17 llr = 221 E-value = 2.5e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 32111:11:aa41:: pos.-specific C 561398:8a:::818 probability G :::6::6::::::2: matrix T 229::241:::6182 bits 2.2 * 1.9 *** 1.7 * *** 1.5 ** *** Relative 1.3 * ** **** * * Entropy 1.1 * ** **** *** (18.7 bits) 0.9 ************* 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CCTGCCGCCAATCTC consensus AT C T A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 10750 437 6.18e-10 TGGAGACGAA CCTGCCGCCAATCTC CAACTACAAG 8511 440 8.93e-09 GCGAGAAGGG CCTGCCGCCAATCTT CACCTACCTC 11089 342 4.11e-08 CCTGGCGAGA CTTCCCTCCAATCTC AAGATGTTCC 3361 297 1.06e-07 AGGCGGGTAA TCTGCCGCCAAACGC CTCTTCGTTG bd856 331 1.24e-07 TTTCTTTCTG ACTACCTCCAATCTC CAATATTCGA bd622 235 1.24e-07 GAACACTCAA CCTCCCTCCAAACGC TCGGCCTCTT 7505 431 1.68e-07 AGCGAGCCAA ACTCCCTCCAATCTT CGGTTCAACA 31062 314 2.50e-07 CTGCTCTCCT CTTGCCTTCAATCTC ATTGTCTCAT 1009 403 4.30e-07 GACTACAAAT CATGCTGCCAATCTT CCGCTGGCGA 1931 408 6.68e-07 AGGAGCTCGT TTTGCCACCAATCTC TTCTCCATCT 6626 5 9.26e-07 ATGC CATGCTGCCAATATC GTCAAGGCAT 4167 278 1.09e-06 CCCTTTCCGA ATTGCCGACAAACTC TCGTCGGAGG 37302 263 1.37e-06 TAGAAAGCTT ACTCCCGCCAATTTT TCACTTCGGC 4491 353 1.97e-06 GGATTTTAAA ACTGATGCCAAACTC CCAAGAGAGG 8110 298 2.58e-06 TTCCTGTGAA CCAACCGCCAAACGC CAAACGCCAA 9055 360 3.16e-06 ACCCTATCTT CACGCCTTCAATCTC TCTGTGTTCA 3123 161 4.29e-06 CCTTTAAAAA TCTCCCGCCAAAACC TGTGCTCAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10750 6.2e-10 436_[+1]_49 8511 8.9e-09 439_[+1]_46 11089 4.1e-08 341_[+1]_144 3361 1.1e-07 296_[+1]_189 bd856 1.2e-07 330_[+1]_155 bd622 1.2e-07 234_[+1]_251 7505 1.7e-07 430_[+1]_55 31062 2.5e-07 313_[+1]_172 1009 4.3e-07 402_[+1]_83 1931 6.7e-07 407_[+1]_78 6626 9.3e-07 4_[+1]_481 4167 1.1e-06 277_[+1]_208 37302 1.4e-06 262_[+1]_223 4491 2e-06 352_[+1]_133 8110 2.6e-06 297_[+1]_188 9055 3.2e-06 359_[+1]_126 3123 4.3e-06 160_[+1]_325 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=17 10750 ( 437) CCTGCCGCCAATCTC 1 8511 ( 440) CCTGCCGCCAATCTT 1 11089 ( 342) CTTCCCTCCAATCTC 1 3361 ( 297) TCTGCCGCCAAACGC 1 bd856 ( 331) ACTACCTCCAATCTC 1 bd622 ( 235) CCTCCCTCCAAACGC 1 7505 ( 431) ACTCCCTCCAATCTT 1 31062 ( 314) CTTGCCTTCAATCTC 1 1009 ( 403) CATGCTGCCAATCTT 1 1931 ( 408) TTTGCCACCAATCTC 1 6626 ( 5) CATGCTGCCAATATC 1 4167 ( 278) ATTGCCGACAAACTC 1 37302 ( 263) ACTCCCGCCAATTTT 1 4491 ( 353) ACTGATGCCAAACTC 1 8110 ( 298) CCAACCGCCAAACGC 1 9055 ( 360) CACGCCTTCAATCTC 1 3123 ( 161) TCTCCCGCCAAAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 22842 bayes= 11.186 E= 2.5e-009 9 119 -1073 -60 -64 134 -1073 -19 -222 -198 -1073 172 -123 34 139 -1073 -222 202 -1073 -1073 -1073 183 -1073 -60 -222 -1073 139 40 -222 183 -1073 -119 -1073 211 -1073 -1073 186 -1073 -1073 -1073 186 -1073 -1073 -1073 36 -1073 -1073 127 -123 183 -1073 -218 -1073 -198 -35 151 -1073 172 -1073 -19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 17 E= 2.5e-009 0.294118 0.529412 0.000000 0.176471 0.176471 0.588235 0.000000 0.235294 0.058824 0.058824 0.000000 0.882353 0.117647 0.294118 0.588235 0.000000 0.058824 0.941176 0.000000 0.000000 0.000000 0.823529 0.000000 0.176471 0.058824 0.000000 0.588235 0.352941 0.058824 0.823529 0.000000 0.117647 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.352941 0.000000 0.000000 0.647059 0.117647 0.823529 0.000000 0.058824 0.000000 0.058824 0.176471 0.764706 0.000000 0.764706 0.000000 0.235294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][CT]T[GC]CC[GT]CCAA[TA]CT[CT] -------------------------------------------------------------------------------- Time 17.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 43 llr = 357 E-value = 1.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 313:21:2:2:: pos.-specific C 1:::::::::1: probability G 5216:1a:6:55 matrix T :66488:84835 bits 2.2 1.9 * 1.7 * 1.5 * Relative 1.3 * ** * Entropy 1.1 **** * * (12.0 bits) 0.9 ******* * 0.6 ********** * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GTTGTTGTGTGT consensus AGAT T TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 3123 20 3.56e-07 TATTTGTATT GTTGTTGTTTGT GGTGGGGATG 7237 94 6.79e-07 GAGCTCTGTC GTTGTTGTGTTT GTCATGTTGG 5401 209 8.50e-07 GATGGAGTGT GGTGTTGTGTGG TGTAATTTGC 1009 326 2.87e-06 GCCGTCCGTC GTTGATGTGTGT TGTGATTTGA 23875 137 4.50e-06 TTAGAAGTGG ATTGTTGTTTTT CTATTTTGAT 4167 145 6.09e-06 CTTCATGATG GTATTTGTGTTT CGGTGTTGGA 21016 10 8.10e-06 CGTCCACTC GTTTTTGTGTCT AATGATGGAC 1243 284 1.05e-05 GATGGAATCA GTTTTGGTGTGG GTTTAGATCT 5192 340 1.21e-05 GGGAGAGGAT GTTTTGGTGTGT ACTAACCTTG 4166 147 1.36e-05 TCATGGTTGA GTTGTAGTGTGT GATGGAGTGT 4491 93 1.53e-05 CACTGTGGTG ATTGTGGTGTGG AAAGGAGGTT 31062 38 1.75e-05 TCACGCGAAC AGATTTGTGTGG GCGGGCTTTT 24282 149 1.75e-05 ATGTGGTAGC GTGTTTGTGTTG CTTCGATTTG 1594 307 1.75e-05 AACGCAACCT ATTGATGTGTTG GCAGCCGTTA 10073 166 1.97e-05 CAGAGGAGAG ATTTTTGTGTCT ATTGGACACA 22484 161 2.47e-05 AACACCATTG AATGTTGTGTTG TCGACTCCAC 1196 187 3.06e-05 TCTCCTCGTA GGTTTTGATTGG TTAGATTCAT 23223 177 3.41e-05 TGTCAGTGCT GTATTTGTTAGT TGCAATGATA 6203 197 3.77e-05 TAACATACTC GCTGTTGTTTGG AACGTGGTAG 37302 206 3.77e-05 TTGTCGTCAG AGAGTTGTTTTG GGGTATCGGA 3361 159 3.77e-05 TAAATGTACC TTTTTTGTTTGT TCCCAGTTAT 5018 16 4.17e-05 TTGTTATAAC AGTTTTGAGTGG ACTATCTTGT 263852 486 4.17e-05 AGTTGATGAT GATGATGTTTGG TAG 4653 238 5.09e-05 AGGTTGCCGT CTATTTGTTTGT CTCTCCTTCA 24466 115 5.62e-05 TGCCATGGTT GATGATGTGTTG TTTGATGGTT 8511 389 6.17e-05 TATCTTTTAA AGTTTTGTTAGG TACAAAAGAA 10750 320 9.69e-05 AACTGAATTA CTTGTTGTGATT TAAAGCATAA 11089 230 1.06e-04 GGCAAAAGTT GTGGTTGATTTT TAGTTAGGAA 9286 138 1.16e-04 TGAGGTGGAT GGTGATGTGATG AGCGCCGGGG 9055 25 1.16e-04 GCTGATCTTC ATGGTTGTTTCT TGCTGATGTG 10106 101 1.16e-04 TTAGTTGTGT ATTGTTATGTGT TCCGAATCAT bd856 299 1.26e-04 GCATAAGATA ATTTATGTTTCT GGGCACATTT 20931 90 1.26e-04 CGAAGGTTCA ATAGATGTGAGT CTAGATGCAT 11548 415 1.26e-04 ACTGAGAGAA GGAGTTGTTTAG TCACTTTGAT 6536 17 1.36e-04 AGTAAAGTGC AGTGTTGTATGG TGACGTGGAG 7505 262 1.73e-04 CGCACCCAAT CTTTTTGATTTG GAGGATGATT 8263 446 2.01e-04 GGCAAGAGAT ATATTTGAGAGT CGAGGCAAAT 1931 186 2.33e-04 TATTGAAATA TTAGTTGTTAGG ATTACTATCA 8110 110 2.50e-04 ATTTCAAAAG GTATTGGAGTTG GCAAGTATCA 39677 482 2.68e-04 GCCCGAGGAA GATATTGTGTTG ACAAATT 261541 59 3.30e-04 CACTGCATAG GAATTAGTTTGT CTTCGGTGCG 1904 208 3.52e-04 GTGCACTACT GGAGTTGAGTAT TGATGGGTGA 1210 94 3.76e-04 CGTGGTGGAG GTGGAAGTTTGT ATCCGCTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3123 3.6e-07 19_[+2]_469 7237 6.8e-07 93_[+2]_395 5401 8.5e-07 208_[+2]_280 1009 2.9e-06 325_[+2]_163 23875 4.5e-06 136_[+2]_352 4167 6.1e-06 144_[+2]_344 21016 8.1e-06 9_[+2]_479 1243 1e-05 283_[+2]_205 5192 1.2e-05 339_[+2]_149 4166 1.4e-05 146_[+2]_342 4491 1.5e-05 92_[+2]_396 31062 1.8e-05 37_[+2]_451 24282 1.8e-05 148_[+2]_340 1594 1.8e-05 306_[+2]_182 10073 2e-05 165_[+2]_323 22484 2.5e-05 160_[+2]_328 1196 3.1e-05 186_[+2]_302 23223 3.4e-05 176_[+2]_312 6203 3.8e-05 196_[+2]_292 37302 3.8e-05 205_[+2]_283 3361 3.8e-05 158_[+2]_330 5018 4.2e-05 15_[+2]_473 263852 4.2e-05 485_[+2]_3 4653 5.1e-05 237_[+2]_251 24466 5.6e-05 114_[+2]_374 8511 6.2e-05 388_[+2]_100 10750 9.7e-05 319_[+2]_169 11089 0.00011 229_[+2]_259 9286 0.00012 137_[+2]_351 9055 0.00012 24_[+2]_464 10106 0.00012 100_[+2]_388 bd856 0.00013 298_[+2]_190 20931 0.00013 89_[+2]_399 11548 0.00013 414_[+2]_74 6536 0.00014 16_[+2]_472 7505 0.00017 261_[+2]_227 8263 0.0002 445_[+2]_43 1931 0.00023 185_[+2]_303 8110 0.00025 109_[+2]_379 39677 0.00027 481_[+2]_7 261541 0.00033 58_[+2]_430 1904 0.00035 207_[+2]_281 1210 0.00038 93_[+2]_395 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=43 3123 ( 20) GTTGTTGTTTGT 1 7237 ( 94) GTTGTTGTGTTT 1 5401 ( 209) GGTGTTGTGTGG 1 1009 ( 326) GTTGATGTGTGT 1 23875 ( 137) ATTGTTGTTTTT 1 4167 ( 145) GTATTTGTGTTT 1 21016 ( 10) GTTTTTGTGTCT 1 1243 ( 284) GTTTTGGTGTGG 1 5192 ( 340) GTTTTGGTGTGT 1 4166 ( 147) GTTGTAGTGTGT 1 4491 ( 93) ATTGTGGTGTGG 1 31062 ( 38) AGATTTGTGTGG 1 24282 ( 149) GTGTTTGTGTTG 1 1594 ( 307) ATTGATGTGTTG 1 10073 ( 166) ATTTTTGTGTCT 1 22484 ( 161) AATGTTGTGTTG 1 1196 ( 187) GGTTTTGATTGG 1 23223 ( 177) GTATTTGTTAGT 1 6203 ( 197) GCTGTTGTTTGG 1 37302 ( 206) AGAGTTGTTTTG 1 3361 ( 159) TTTTTTGTTTGT 1 5018 ( 16) AGTTTTGAGTGG 1 263852 ( 486) GATGATGTTTGG 1 4653 ( 238) CTATTTGTTTGT 1 24466 ( 115) GATGATGTGTTG 1 8511 ( 389) AGTTTTGTTAGG 1 10750 ( 320) CTTGTTGTGATT 1 11089 ( 230) GTGGTTGATTTT 1 9286 ( 138) GGTGATGTGATG 1 9055 ( 25) ATGGTTGTTTCT 1 10106 ( 101) ATTGTTATGTGT 1 bd856 ( 299) ATTTATGTTTCT 1 20931 ( 90) ATAGATGTGAGT 1 11548 ( 415) GGAGTTGTTTAG 1 6536 ( 17) AGTGTTGTATGG 1 7505 ( 262) CTTTTTGATTTG 1 8263 ( 446) ATATTTGAGAGT 1 1931 ( 186) TTAGTTGTTAGG 1 8110 ( 110) GTATTGGAGTTG 1 39677 ( 482) GATATTGTGTTG 1 261541 ( 59) GAATTAGTTTGT 1 1904 ( 208) GGAGTTGAGTAT 1 1210 ( 94) GTGGAAGTTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 22983 bayes= 9.39021 E= 1.4e-005 34 -173 125 -252 -124 -331 5 123 2 -1207 -127 123 -356 -1207 131 64 -57 -1207 -1207 160 -198 -1207 -127 164 -356 -1207 212 -1207 -76 -1207 -1207 164 -356 -1207 131 64 -76 -1207 -1207 164 -256 -132 125 28 -1207 -1207 112 93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 43 E= 1.4e-005 0.348837 0.069767 0.534884 0.046512 0.116279 0.023256 0.232558 0.627907 0.279070 0.000000 0.093023 0.627907 0.023256 0.000000 0.558140 0.418605 0.186047 0.000000 0.000000 0.813953 0.069767 0.000000 0.093023 0.837209 0.023256 0.000000 0.976744 0.000000 0.162791 0.000000 0.000000 0.837209 0.023256 0.000000 0.558140 0.418605 0.162791 0.000000 0.000000 0.837209 0.046512 0.093023 0.534884 0.325581 0.000000 0.000000 0.488372 0.511628 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][TG][TA][GT]TTGT[GT]T[GT][TG] -------------------------------------------------------------------------------- Time 34.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 25 llr = 297 E-value = 4.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 39:267718256175293186 pos.-specific C 71383114:8428117:3614 probability G ::3::::2:::1:11::2::: matrix T ::4::1232:1:1121:22:: bits 2.2 1.9 1.7 1.5 * Relative 1.3 * * ** * * Entropy 1.1 ** * ** * * * (17.2 bits) 0.9 ** ** ** * ** *** 0.6 ** **** ** * ** *** 0.4 ** **** ****** ** *** 0.2 ***************** *** 0.0 --------------------- Multilevel CATCAAACACAACAACAACAA consensus A C C TT ACC T CT C sequence G G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9055 478 3.11e-09 CATCGCAAAC CATCAAACAACACATCATCAA CC 24282 438 1.04e-08 ATACTACGTA CACCTAATACAACAACAGCAA CAACTCACCG 37302 464 1.56e-08 ACAAATAGAT CATCATACACACCAACAATAC CCCAAGCAAC 10106 271 5.61e-08 TTGCACCAGC CCTCCAATACCACATCAATAA CTCCCGGCTA 1210 283 1.59e-07 GCCAGCCAAG AATCAATCAATACAACAGCAA AGATGGAATA 3123 399 2.21e-07 CTCTAAAAAG CAGCAAAGACCCCAACAGTGA AGCCTTCACC 11548 467 3.04e-07 CAGTAGTCAG AAGCAAAGTCAGCATCATCAA CAATCGCCTA 5018 356 3.37e-07 TACAGTACAA CAGCAACTACAACACTATCAC TCGATTATCT 6204 441 4.14e-07 TTTGTGCTCT AATCAACCACCACTTCAATAC CAATACTCGC 23223 476 5.07e-07 CATCCGACAA CACCAAAGACGACGATACCAA TCCA 11089 469 9.07e-07 TAACACTGTA CAGACAAAACAACAGAAACAA CAAACAGCCA 4166 473 1.20e-06 AAGTAACATC AATCCAACACCGAAACACAAA TACCATC 5192 475 1.31e-06 CACAACGTAC CCCAATATACAACAACAGTAC GCGAT 10073 291 1.31e-06 GTGACATCTA AACAAAAGAAACCAGCAGCAC TTCGCACCTG 1931 267 1.57e-06 AACGAAGCTT CATCCAAAAAAACAAAAACAG ACTGTGATTT 22484 80 2.43e-06 AATATCGCAT CACCCTTTACCGCATCACAAA CTCTCATTAT 6536 178 2.65e-06 GTGGTGTTGC CAGCAGTTACCCCGACATCAA TGTAAAGCGA 4167 479 2.65e-06 TGACACACTC CATCACACACTACAACTCAAC C 7237 449 3.13e-06 AATTCAATAT CAGCCATCAAACCTTCACCCC AGAGAAAACC 1243 27 4.34e-06 GAACACCTTA CAAAAAAGACAACCCAACCAA AGAGCATAGT 8511 469 5.09e-06 TACCTCCACA CATCCCTCTCAATCACAACAC TCAGCACAAC 1594 460 7.49e-06 CAAGTCAGTG AAGCACATACCAATACAACCA GCAACATCAG 8263 283 8.08e-06 CTTACAAACG CACCAACGACAATAGTACCCC CCCCCAACAC 20931 473 9.37e-06 AAATATCAAC ACCCCAACTCAACCCAACCAC TGTCAAG bd856 390 1.01e-05 TCACAAAATC CATCAAACTACTCAACCATAA ATCGTCATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9055 3.1e-09 477_[+3]_2 24282 1e-08 437_[+3]_42 37302 1.6e-08 463_[+3]_16 10106 5.6e-08 270_[+3]_209 1210 1.6e-07 282_[+3]_197 3123 2.2e-07 398_[+3]_81 11548 3e-07 466_[+3]_13 5018 3.4e-07 355_[+3]_124 6204 4.1e-07 440_[+3]_39 23223 5.1e-07 475_[+3]_4 11089 9.1e-07 468_[+3]_11 4166 1.2e-06 472_[+3]_7 5192 1.3e-06 474_[+3]_5 10073 1.3e-06 290_[+3]_189 1931 1.6e-06 266_[+3]_213 22484 2.4e-06 79_[+3]_400 6536 2.7e-06 177_[+3]_302 4167 2.7e-06 478_[+3]_1 7237 3.1e-06 448_[+3]_31 1243 4.3e-06 26_[+3]_453 8511 5.1e-06 468_[+3]_11 1594 7.5e-06 459_[+3]_20 8263 8.1e-06 282_[+3]_197 20931 9.4e-06 472_[+3]_7 bd856 1e-05 389_[+3]_90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=25 9055 ( 478) CATCAAACAACACATCATCAA 1 24282 ( 438) CACCTAATACAACAACAGCAA 1 37302 ( 464) CATCATACACACCAACAATAC 1 10106 ( 271) CCTCCAATACCACATCAATAA 1 1210 ( 283) AATCAATCAATACAACAGCAA 1 3123 ( 399) CAGCAAAGACCCCAACAGTGA 1 11548 ( 467) AAGCAAAGTCAGCATCATCAA 1 5018 ( 356) CAGCAACTACAACACTATCAC 1 6204 ( 441) AATCAACCACCACTTCAATAC 1 23223 ( 476) CACCAAAGACGACGATACCAA 1 11089 ( 469) CAGACAAAACAACAGAAACAA 1 4166 ( 473) AATCCAACACCGAAACACAAA 1 5192 ( 475) CCCAATATACAACAACAGTAC 1 10073 ( 291) AACAAAAGAAACCAGCAGCAC 1 1931 ( 267) CATCCAAAAAAACAAAAACAG 1 22484 ( 80) CACCCTTTACCGCATCACAAA 1 6536 ( 178) CAGCAGTTACCCCGACATCAA 1 4167 ( 479) CATCACACACTACAACTCAAC 1 7237 ( 449) CAGCCATCAAACCTTCACCCC 1 1243 ( 27) CAAAAAAGACAACCCAACCAA 1 8511 ( 469) CATCCCTCTCAATCACAACAC 1 1594 ( 460) AAGCACATACCAATACAACCA 1 8263 ( 283) CACCAACGACAATAGTACCCC 1 20931 ( 473) ACCCCAACTCAACCCAACCAC 1 bd856 ( 390) CATCAAACTACTCAACCATAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22560 bayes= 10.3065 E= 4.5e-006 2 163 -1129 -1129 168 -95 -1129 -1129 -278 27 32 58 -78 186 -1129 -1129 122 46 -1129 -274 139 -95 -249 -116 130 -95 -1129 -42 -178 79 9 6 161 -1129 -1129 -74 -20 171 -1129 -1129 92 63 -249 -174 122 -21 -91 -274 -178 186 -1129 -174 130 -95 -149 -116 92 -95 -91 -16 -78 163 -1129 -116 174 -253 -1129 -274 22 46 -17 -74 -120 146 -1129 -16 161 -95 -249 -1129 102 79 -249 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 25 E= 4.5e-006 0.280000 0.720000 0.000000 0.000000 0.880000 0.120000 0.000000 0.000000 0.040000 0.280000 0.280000 0.400000 0.160000 0.840000 0.000000 0.000000 0.640000 0.320000 0.000000 0.040000 0.720000 0.120000 0.040000 0.120000 0.680000 0.120000 0.000000 0.200000 0.080000 0.400000 0.240000 0.280000 0.840000 0.000000 0.000000 0.160000 0.240000 0.760000 0.000000 0.000000 0.520000 0.360000 0.040000 0.080000 0.640000 0.200000 0.120000 0.040000 0.080000 0.840000 0.000000 0.080000 0.680000 0.120000 0.080000 0.120000 0.520000 0.120000 0.120000 0.240000 0.160000 0.720000 0.000000 0.120000 0.920000 0.040000 0.000000 0.040000 0.320000 0.320000 0.200000 0.160000 0.120000 0.640000 0.000000 0.240000 0.840000 0.120000 0.040000 0.000000 0.560000 0.400000 0.040000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA]A[TCG]C[AC]A[AT][CTG]A[CA][AC][AC]CA[AT]CA[ACG][CT]A[AC] -------------------------------------------------------------------------------- Time 50.72 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10073 1.27e-04 165_[+2(1.97e-05)]_113_\ [+3(1.31e-06)]_124_[+3(2.31e-05)]_44 1009 2.36e-05 325_[+2(2.87e-06)]_65_\ [+1(4.30e-07)]_83 10106 1.87e-05 270_[+3(5.61e-08)]_209 10750 2.38e-06 319_[+2(9.69e-05)]_105_\ [+1(6.18e-10)]_49 11089 1.12e-07 341_[+1(4.11e-08)]_48_\ [+3(9.06e-05)]_43_[+3(9.07e-07)]_11 11548 2.99e-04 466_[+3(3.04e-07)]_13 1196 6.11e-02 186_[+2(3.06e-05)]_302 1210 4.94e-04 250_[+3(2.31e-05)]_11_\ [+3(1.59e-07)]_197 1243 8.16e-04 26_[+3(4.34e-06)]_236_\ [+2(1.05e-05)]_205 1594 7.56e-04 282_[+3(8.58e-05)]_3_[+2(1.75e-05)]_\ 141_[+3(7.49e-06)]_20 1904 3.52e-01 500 1931 4.50e-06 266_[+3(1.57e-06)]_120_\ [+1(6.68e-07)]_35_[+3(8.58e-05)]_22 20931 3.11e-03 472_[+3(9.37e-06)]_7 21016 1.93e-02 9_[+2(8.10e-06)]_296_[+2(5.09e-05)]_\ 171 22484 3.54e-04 79_[+3(2.43e-06)]_60_[+2(2.47e-05)]_\ 305_[+3(5.49e-05)]_2 23223 2.54e-04 176_[+2(3.41e-05)]_287_\ [+3(5.07e-07)]_4 23875 1.34e-02 136_[+2(4.50e-06)]_352 24282 6.08e-06 148_[+2(1.75e-05)]_84_\ [+2(9.69e-05)]_21_[+2(8.20e-05)]_148_[+3(1.04e-08)]_42 24466 1.28e-01 114_[+2(5.62e-05)]_374 261541 5.02e-01 500 263271 4.39e-01 500 263852 2.52e-01 485_[+2(4.17e-05)]_3 31062 1.06e-04 37_[+2(1.75e-05)]_264_\ [+1(2.50e-07)]_172 3123 1.20e-08 19_[+2(3.56e-07)]_129_\ [+1(4.29e-06)]_223_[+3(2.21e-07)]_81 3361 1.10e-05 158_[+2(3.77e-05)]_126_\ [+1(1.06e-07)]_189 37302 2.66e-08 205_[+2(3.77e-05)]_45_\ [+1(1.37e-06)]_130_[+1(8.42e-05)]_41_[+3(1.56e-08)]_16 39677 1.39e-01 500 4166 2.80e-04 146_[+2(1.36e-05)]_314_\ [+3(1.20e-06)]_7 4167 4.46e-07 144_[+2(6.09e-06)]_121_\ [+1(1.09e-06)]_59_[+3(2.99e-05)]_106_[+3(2.65e-06)]_1 4491 9.88e-05 92_[+2(1.53e-05)]_248_\ [+1(1.97e-06)]_133 4653 5.67e-02 237_[+2(5.09e-05)]_251 5018 4.51e-05 15_[+2(4.17e-05)]_328_\ [+3(3.37e-07)]_124 5192 1.54e-04 339_[+2(1.21e-05)]_123_\ [+3(1.31e-06)]_5 5401 1.15e-02 208_[+2(8.50e-07)]_280 6203 4.60e-02 196_[+2(3.77e-05)]_292 6204 5.81e-04 440_[+3(4.14e-07)]_39 6536 2.20e-03 177_[+3(2.65e-06)]_302 6626 2.46e-03 4_[+1(9.26e-07)]_481 7237 2.99e-06 32_[+2(1.53e-05)]_49_[+2(6.79e-07)]_\ 343_[+3(3.13e-06)]_5_[+3(6.89e-05)]_5 7505 4.57e-04 430_[+1(1.68e-07)]_55 8110 4.04e-03 297_[+1(2.58e-06)]_188 8263 1.97e-03 282_[+3(8.08e-06)]_197 8511 8.25e-08 388_[+2(6.17e-05)]_39_\ [+1(8.93e-09)]_14_[+3(5.09e-06)]_11 9055 3.57e-08 359_[+1(3.16e-06)]_103_\ [+3(3.11e-09)]_2 9286 1.69e-01 500 bd622 7.23e-04 234_[+1(1.24e-07)]_251 bd856 3.10e-06 330_[+1(1.24e-07)]_44_\ [+3(1.01e-05)]_90 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************