******************************************************************************** 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/86/86.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11492 1.0000 500 11799 1.0000 500 17008 1.0000 500 21260 1.0000 500 22667 1.0000 500 23734 1.0000 500 25104 1.0000 500 25526 1.0000 500 25772 1.0000 500 261293 1.0000 500 261635 1.0000 500 262513 1.0000 500 263415 1.0000 500 264672 1.0000 500 269714 1.0000 500 28317 1.0000 500 30105 1.0000 500 32223 1.0000 500 34379 1.0000 500 35372 1.0000 500 3579 1.0000 500 37328 1.0000 500 37441 1.0000 500 3787 1.0000 500 39802 1.0000 500 4830 1.0000 500 7942 1.0000 500 9238 1.0000 500 961 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/86/86.seqs.fa -oc motifs/86 -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= 29 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= 14500 N= 29 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.243 G 0.227 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.243 G 0.227 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 23 llr = 271 E-value = 6.8e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 6:7263345542462831931 pos.-specific C 372735755238428159:37 probability G :::1:2:::22:1:::1::1: matrix T :21::::::11::2::::131 bits 2.1 1.9 1.7 * 1.5 ** Relative 1.3 * * * ** Entropy 1.1 * * * * * ** ** (17.0 bits) 0.9 **** * * * ** ** 0.6 ***** *** * *** ** * 0.4 ********* ******** * 0.2 ******************* * 0.0 --------------------- Multilevel ACACACCCAAACCACACCATC consensus CT CAAACGC AC A C sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25772 465 7.29e-10 ACACACACAC ACACACCCACACACCACCACC TCTCTTTATC 21260 225 7.30e-09 TCACTTATTC ATACCGCCAAACAACAACATC AGCAGCAGTA 11799 187 2.24e-08 ATGTCTGTGT ACACAACCACACCACACCTCC CTTCGCGATG 9238 480 8.90e-08 CTAGCAGTAC ACACACACAGGCAACATCATC 4830 480 1.12e-07 GCCTCTCTTC ACACCCAACGACAACACAACC 22667 456 1.41e-07 TACACCTCCG ATACCCACCACCCACCACATC AATCTCGCAT 39802 476 1.97e-07 TACTACTACT ACACTACACAACCAAAACACC CAAC 37441 2 1.97e-07 G ACAGACCACATCATCACCAAC ACGAGGAGGC 261635 479 2.19e-07 TTCACCTCTG ATACACCACCAACACAACAGC C 25104 299 7.43e-07 TCGCTCGCCC CCCCCCCCAACCATCACCATG ACCATGAGAC 269714 360 8.17e-07 CTTTCTCAAG CTACAGCAAGACCACAGCATA GTTTCCAACG 32223 426 1.85e-06 CCACTGTTCA ACAACACCATACACCACCAAT ACTACTACTG 3787 466 2.02e-06 CTTATCAAAA ACAAAACACACCTACACCTTC CATTTGCAAA 264672 231 2.40e-06 TCCTTCAACT CCACATCCAATCCACAACAGT CAAATGCTAC 34379 202 3.62e-06 AGCAAGCCCC CCCCCCCAATGCGACAACAAA GACAGACAGA 35372 445 4.60e-06 ACACTCCTTC ACCAACACACGACAAACCACC ATAACGCTCC 263415 479 4.60e-06 ATCACACTGA ACAAACAGCACACCCAACAAC C 3579 442 4.98e-06 CTTCCTCTGC CCTCCGCTCAGCCTCACCAAC AACTCCCGGC 262513 462 8.44e-06 CTCGGCATTG CTACAACACACCCTCCGCATT GGCATCTCAC 28317 118 9.76e-06 CCACTTAAAG CCAGAGAAAACAGCCACCAAC GGGAGTACAA 7942 366 1.12e-05 GCAATGGTGT CCCCCCCCCGGCAAAGCCACA AGGCGAAGCC 25526 183 1.39e-05 ACCATCAGCC ACTCGCCCAGACACACACACC CTCCTCGTAC 23734 480 3.02e-05 AGCTGCCTTC TAACAACCCAACGACAGAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25772 7.3e-10 464_[+1]_15 21260 7.3e-09 224_[+1]_255 11799 2.2e-08 186_[+1]_293 9238 8.9e-08 479_[+1] 4830 1.1e-07 479_[+1] 22667 1.4e-07 455_[+1]_24 39802 2e-07 475_[+1]_4 37441 2e-07 1_[+1]_478 261635 2.2e-07 478_[+1]_1 25104 7.4e-07 298_[+1]_181 269714 8.2e-07 359_[+1]_120 32223 1.9e-06 425_[+1]_54 3787 2e-06 465_[+1]_14 264672 2.4e-06 230_[+1]_249 34379 3.6e-06 201_[+1]_278 35372 4.6e-06 444_[+1]_35 263415 4.6e-06 478_[+1]_1 3579 5e-06 441_[+1]_38 262513 8.4e-06 461_[+1]_18 28317 9.8e-06 117_[+1]_362 7942 1.1e-05 365_[+1]_114 25526 1.4e-05 182_[+1]_297 23734 3e-05 479_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=23 25772 ( 465) ACACACCCACACACCACCACC 1 21260 ( 225) ATACCGCCAAACAACAACATC 1 11799 ( 187) ACACAACCACACCACACCTCC 1 9238 ( 480) ACACACACAGGCAACATCATC 1 4830 ( 480) ACACCCAACGACAACACAACC 1 22667 ( 456) ATACCCACCACCCACCACATC 1 39802 ( 476) ACACTACACAACCAAAACACC 1 37441 ( 2) ACAGACCACATCATCACCAAC 1 261635 ( 479) ATACACCACCAACACAACAGC 1 25104 ( 299) CCCCCCCCAACCATCACCATG 1 269714 ( 360) CTACAGCAAGACCACAGCATA 1 32223 ( 426) ACAACACCATACACCACCAAT 1 3787 ( 466) ACAAAACACACCTACACCTTC 1 264672 ( 231) CCACATCCAATCCACAACAGT 1 34379 ( 202) CCCCCCCAATGCGACAACAAA 1 35372 ( 445) ACCAACACACGACAAACCACC 1 263415 ( 479) ACAAACAGCACACCCAACAAC 1 3579 ( 442) CCTCCGCTCAGCCTCACCAAC 1 262513 ( 462) CTACAACACACCCTCCGCATT 1 28317 ( 118) CCAGAGAAAACAGCCACCAAC 1 7942 ( 366) CCCCCCCCCGGCAAAGCCACA 1 25526 ( 183) ACTCGCCCAGACACACACACC 1 23734 ( 480) TAACAACCCAACGACAGAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 9.64205 E= 6.8e-009 122 52 -1117 -263 -258 161 -1117 -31 150 -48 -1117 -163 -59 161 -138 -1117 111 52 -238 -263 0 110 -38 -263 0 161 -1117 -1117 58 110 -238 -263 100 98 -1117 -1117 100 -48 -6 -163 73 10 -6 -163 -59 177 -1117 -1117 58 84 -80 -263 122 -16 -1117 -63 -59 177 -1117 -1117 166 -90 -238 -1117 41 98 -80 -263 -159 191 -1117 -1117 180 -1117 -1117 -163 0 33 -138 37 -100 152 -238 -105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 23 E= 6.8e-009 0.608696 0.347826 0.000000 0.043478 0.043478 0.739130 0.000000 0.217391 0.739130 0.173913 0.000000 0.086957 0.173913 0.739130 0.086957 0.000000 0.565217 0.347826 0.043478 0.043478 0.260870 0.521739 0.173913 0.043478 0.260870 0.739130 0.000000 0.000000 0.391304 0.521739 0.043478 0.043478 0.521739 0.478261 0.000000 0.000000 0.521739 0.173913 0.217391 0.086957 0.434783 0.260870 0.217391 0.086957 0.173913 0.826087 0.000000 0.000000 0.391304 0.434783 0.130435 0.043478 0.608696 0.217391 0.000000 0.173913 0.173913 0.826087 0.000000 0.000000 0.826087 0.130435 0.043478 0.000000 0.347826 0.478261 0.130435 0.043478 0.086957 0.913043 0.000000 0.000000 0.913043 0.000000 0.000000 0.086957 0.260870 0.304348 0.086957 0.347826 0.130435 0.695652 0.043478 0.130435 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][CT]AC[AC][CA][CA][CA][AC][AG][ACG]C[CA][AC]CA[CA]CA[TCA]C -------------------------------------------------------------------------------- Time 7.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 20 llr = 235 E-value = 1.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3611:::33:3773611356 pos.-specific C :3143:12:2:111:::12:: probability G 8324:8194197338268353 matrix T 3222729:352::::241312 bits 2.1 1.9 1.7 1.5 * * Relative 1.3 * *** * * Entropy 1.1 * *** * * * (17.0 bits) 0.9 * **** ***** ** 0.6 * **** ******** ** 0.4 * * ***** ******** ** 0.2 * **************** ** 0.0 --------------------- Multilevel GAACTGTGGTGGAAGAGGGAA consensus TCGGCT AA AGGAGT TGG sequence G T TC T A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 269714 198 3.41e-10 TTCAGAAGTA GTACTGTGGTGGAGGAGGCGA GGTTGGCAGA 262513 99 5.65e-09 CTGACTGTTT GGACCGTGTTGGAAGAGGTGT GCTTTGCCGA 261635 91 1.06e-08 GATGAGAGAA GCACCGTGTAGGAAGATGAAA GTAGACTCCA 17008 226 2.52e-08 GATGTGAGAT GGACTGTGATTGAAGATGTGG ATGCTAAGAA 11799 37 1.86e-07 TGGCGTAATG GTAGTGTGGAGGAAGGGAGGG GTTGTGGTGG 25526 314 6.61e-07 TCCGGCGCTT GGACTGTGGCGGACGATTTGA CGGAGCTCAT 263415 38 8.03e-07 CGGTGCATCG GTTGTGTGTCGGAAGTAGGGA GTGGCGGCTT 4830 262 1.17e-06 AGTACTCCCT GAAGTGTGAAGACAGAGGCTA TCAGTAGCAC 21260 92 1.17e-06 AGGTCACCCA TCATTGTCTTGGGAGAGGTAT TGTCATATCC 35372 257 1.84e-06 CATTTCGACG GGACTGTGGAGAGAAGGGATG AACTACAGGC 11492 51 1.84e-06 CTATGATGAG TCGATTTGGTGAAAGATGAAA TTATGAGGTA 3787 189 3.06e-06 AATTACTATA TACCTGTGGTGAAAAGTGTAA TTATGGGACA 25104 123 3.06e-06 TGTGGTCTCA TATGTGTCGTGGAGGAGCGAA TCAACGATAA 37441 223 4.23e-06 GGTTGATACA GTGGCTTCATGGAGGTTGGGA TGGTGTGCGA 261293 120 5.34e-06 TGTCAGGTGG GAATTGCGTATGAAAAGGCAA AGCGTGTTAT 3579 17 7.21e-06 TAATGACTGT TCAGTGTGACGCGGAAGGAGT GTGGGATTCA 25772 264 7.76e-06 ATGTGGAACT GGATTTGGGGGAAAGAGGGAG TCTGAGTTTG 264672 435 1.11e-05 TAACAGCTTA GAGGAGTGTTGCGGGTTGTAA ATGAATGACA 30105 307 1.27e-05 GAGAGTGAGA GAGACGTGATTGGAGGGTGAA TTGCCCATGA 23734 2 1.36e-05 G GCTTCTTGACGGAGATGGAGG CTGATGTCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269714 3.4e-10 197_[+2]_282 262513 5.6e-09 98_[+2]_381 261635 1.1e-08 90_[+2]_389 17008 2.5e-08 225_[+2]_254 11799 1.9e-07 36_[+2]_443 25526 6.6e-07 313_[+2]_166 263415 8e-07 37_[+2]_442 4830 1.2e-06 261_[+2]_218 21260 1.2e-06 91_[+2]_388 35372 1.8e-06 256_[+2]_223 11492 1.8e-06 50_[+2]_429 3787 3.1e-06 188_[+2]_291 25104 3.1e-06 122_[+2]_357 37441 4.2e-06 222_[+2]_257 261293 5.3e-06 119_[+2]_360 3579 7.2e-06 16_[+2]_463 25772 7.8e-06 263_[+2]_216 264672 1.1e-05 434_[+2]_45 30105 1.3e-05 306_[+2]_173 23734 1.4e-05 1_[+2]_478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=20 269714 ( 198) GTACTGTGGTGGAGGAGGCGA 1 262513 ( 99) GGACCGTGTTGGAAGAGGTGT 1 261635 ( 91) GCACCGTGTAGGAAGATGAAA 1 17008 ( 226) GGACTGTGATTGAAGATGTGG 1 11799 ( 37) GTAGTGTGGAGGAAGGGAGGG 1 25526 ( 314) GGACTGTGGCGGACGATTTGA 1 263415 ( 38) GTTGTGTGTCGGAAGTAGGGA 1 4830 ( 262) GAAGTGTGAAGACAGAGGCTA 1 21260 ( 92) TCATTGTCTTGGGAGAGGTAT 1 35372 ( 257) GGACTGTGGAGAGAAGGGATG 1 11492 ( 51) TCGATTTGGTGAAAGATGAAA 1 3787 ( 189) TACCTGTGGTGAAAAGTGTAA 1 25104 ( 123) TATGTGTCGTGGAGGAGCGAA 1 37441 ( 223) GTGGCTTCATGGAGGTTGGGA 1 261293 ( 120) GAATTGCGTATGAAAAGGCAA 1 3579 ( 17) TCAGTGTGACGCGGAAGGAGT 1 25772 ( 264) GGATTTGGGGGAAAGAGGGAG 1 264672 ( 435) GAGGAGTGTTGCGGGTTGTAA 1 30105 ( 307) GAGACGTGATTGGAGGGTGAA 1 23734 ( 2) GCTTCTTGACGGAGATGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 10.3853 E= 1.0e-002 -1097 -1097 173 -11 20 4 14 -43 120 -228 -18 -84 -138 53 63 -43 -238 4 -1097 138 -1097 -1097 182 -43 -1097 -228 -218 174 -1097 -69 191 -1097 20 -1097 82 16 -6 -28 -218 89 -1097 -1097 191 -84 -6 -128 152 -1097 142 -228 14 -1097 131 -228 40 -1097 -6 -1097 173 -1097 120 -1097 -18 -43 -238 -1097 140 38 -238 -228 182 -143 -6 -69 40 16 78 -1097 99 -143 120 -1097 14 -84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 1.0e-002 0.000000 0.000000 0.750000 0.250000 0.300000 0.250000 0.250000 0.200000 0.600000 0.050000 0.200000 0.150000 0.100000 0.350000 0.350000 0.200000 0.050000 0.250000 0.000000 0.700000 0.000000 0.000000 0.800000 0.200000 0.000000 0.050000 0.050000 0.900000 0.000000 0.150000 0.850000 0.000000 0.300000 0.000000 0.400000 0.300000 0.250000 0.200000 0.050000 0.500000 0.000000 0.000000 0.850000 0.150000 0.250000 0.100000 0.650000 0.000000 0.700000 0.050000 0.250000 0.000000 0.650000 0.050000 0.300000 0.000000 0.250000 0.000000 0.750000 0.000000 0.600000 0.000000 0.200000 0.200000 0.050000 0.000000 0.600000 0.350000 0.050000 0.050000 0.800000 0.100000 0.250000 0.150000 0.300000 0.300000 0.450000 0.000000 0.450000 0.100000 0.600000 0.000000 0.250000 0.150000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][ACGT][AG][CGT][TC][GT]TG[GAT][TAC]G[GA][AG][AG][GA][AGT][GT]G[GTA][AG][AG] -------------------------------------------------------------------------------- Time 13.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 20 llr = 230 E-value = 3.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2224312::31421a:13 pos.-specific C 1251:2:1:1:122:3::2: probability G 68329139:3a34174:272 matrix T 4116:44:97:3451318:6 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * ** * ** Entropy 1.1 * * ** * ** (16.6 bits) 0.9 ** * **** * *** 0.6 ** * **** * *** 0.4 ** * ***** * **** 0.2 *********** ******** 0.0 -------------------- Multilevel GGCTGATGTTGAGTGGATGT consensus T GA TA G GTAAT GCA sequence A G TC C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 263415 236 2.48e-09 CATCATCTCT GGCAGAGGTTGGTTGCATGT CGAGTGTCTC 30105 79 8.70e-08 AAAAGGGATT GGCTGTAGTTGTCAGTATAT GATACGAGGT 23734 31 8.70e-08 GGCTGATGTC GCATGATGTGGGTAGGATGT GAACAGGGCG 37441 303 1.28e-07 GCCTTCTTGA TTGTGTGGTTGTGTGGATGT TATTACCCCC 961 291 1.46e-07 CTCCTGTGTA TCCTAATGTTGGGAGGATGT TTCCTGGTAC 261293 250 1.86e-07 ACTCTCCACC GGCTGATCTTGGCAAGATGT ACATGCCTTC 261635 9 2.37e-07 TGTGGCGG TGCCGTTGTTGTTTGGAGGA TATTCTCGAG 17008 302 3.76e-07 TCTTTGTAAG TGGAGTAGTTGGAAGTATGT TGGGGTCTTA 9238 100 6.47e-07 GCGGTGGCTG GGCTGTGCTTGCTTGTATCT GTCCCGTCAC 11492 75 9.75e-07 GATGAAATTA TGAGGTAGATGAGTGTATGA GTACACGATG 37328 153 1.31e-06 TGGCGGCGGT GGGTGAAGTTGAGCTGAGGA GATCGCTGCT 262513 327 2.29e-06 CGACATGAGC GGCTACGGTGGTGAGTATCG CATTGAGTTC 4830 164 2.74e-06 CTTTCGTGTT GGAAGCAGTTGTTTGGAGAT CGGCCCATGT 28317 44 3.86e-06 GTTTGCTATT GGCGGTGGTGGAGCTCATCT CTTCTTTTGC 22667 143 8.53e-06 CGTTCCCTAC TGAAGATGATGCCCGTATGA ATCGCTTAGA 3787 72 1.51e-05 CAGTTACCGC TGGTGATATTGACTACATCG TTGTGTCTTC 35372 6 1.73e-05 TCGCT TGTGAATGTGGTGAACATGG TACGTGTTAG 269714 235 2.11e-05 CAGAAATGAA CGGTGGAGTTGGTGACATGT CACACTGACG 3579 180 2.72e-05 GTAATCAGGA GGTTGCGGTGGAGTGATTGG GTTGACTGTA 264672 335 3.90e-05 TTCAATGATC GCCCGTTGACGATTGGAGGA GAGGATGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263415 2.5e-09 235_[+3]_245 30105 8.7e-08 78_[+3]_402 23734 8.7e-08 30_[+3]_450 37441 1.3e-07 302_[+3]_178 961 1.5e-07 290_[+3]_190 261293 1.9e-07 249_[+3]_231 261635 2.4e-07 8_[+3]_472 17008 3.8e-07 301_[+3]_179 9238 6.5e-07 99_[+3]_381 11492 9.8e-07 74_[+3]_406 37328 1.3e-06 152_[+3]_328 262513 2.3e-06 326_[+3]_154 4830 2.7e-06 163_[+3]_317 28317 3.9e-06 43_[+3]_437 22667 8.5e-06 142_[+3]_338 3787 1.5e-05 71_[+3]_409 35372 1.7e-05 5_[+3]_475 269714 2.1e-05 234_[+3]_246 3579 2.7e-05 179_[+3]_301 264672 3.9e-05 334_[+3]_146 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=20 263415 ( 236) GGCAGAGGTTGGTTGCATGT 1 30105 ( 79) GGCTGTAGTTGTCAGTATAT 1 23734 ( 31) GCATGATGTGGGTAGGATGT 1 37441 ( 303) TTGTGTGGTTGTGTGGATGT 1 961 ( 291) TCCTAATGTTGGGAGGATGT 1 261293 ( 250) GGCTGATCTTGGCAAGATGT 1 261635 ( 9) TGCCGTTGTTGTTTGGAGGA 1 17008 ( 302) TGGAGTAGTTGGAAGTATGT 1 9238 ( 100) GGCTGTGCTTGCTTGTATCT 1 11492 ( 75) TGAGGTAGATGAGTGTATGA 1 37328 ( 153) GGGTGAAGTTGAGCTGAGGA 1 262513 ( 327) GGCTACGGTGGTGAGTATCG 1 4830 ( 164) GGAAGCAGTTGTTTGGAGAT 1 28317 ( 44) GGCGGTGGTGGAGCTCATCT 1 22667 ( 143) TGAAGATGATGCCCGTATGA 1 3787 ( 72) TGGTGATATTGACTACATCG 1 35372 ( 6) TGTGAATGTGGTGAACATGG 1 269714 ( 235) CGGTGGAGTTGGTGACATGT 1 3579 ( 180) GGTTGCGGTGGAGTGATTGG 1 264672 ( 335) GCCCGTTGACGATTGGAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 13949 bayes= 9.69575 E= 3.7e-003 -1097 -228 128 57 -1097 -69 182 -243 -39 89 14 -143 -39 -128 -59 103 -80 -1097 191 -1097 61 -69 -218 57 20 -1097 40 57 -238 -128 191 -1097 -80 -1097 -1097 166 -1097 -228 14 138 -1097 -1097 214 -1097 20 -128 40 16 -238 -28 82 38 42 -69 -218 74 -39 -1097 163 -143 -238 4 82 16 186 -1097 -1097 -243 -1097 -1097 -18 157 -138 -28 163 -1097 -6 -1097 -18 103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 20 E= 3.7e-003 0.000000 0.050000 0.550000 0.400000 0.000000 0.150000 0.800000 0.050000 0.200000 0.450000 0.250000 0.100000 0.200000 0.100000 0.150000 0.550000 0.150000 0.000000 0.850000 0.000000 0.400000 0.150000 0.050000 0.400000 0.300000 0.000000 0.300000 0.400000 0.050000 0.100000 0.850000 0.000000 0.150000 0.000000 0.000000 0.850000 0.000000 0.050000 0.250000 0.700000 0.000000 0.000000 1.000000 0.000000 0.300000 0.100000 0.300000 0.300000 0.050000 0.200000 0.400000 0.350000 0.350000 0.150000 0.050000 0.450000 0.200000 0.000000 0.700000 0.100000 0.050000 0.250000 0.400000 0.300000 0.950000 0.000000 0.000000 0.050000 0.000000 0.000000 0.200000 0.800000 0.100000 0.200000 0.700000 0.000000 0.250000 0.000000 0.200000 0.550000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT]G[CGA][TA]G[AT][TAG]GT[TG]G[AGT][GTC][TA][GA][GTC]A[TG][GC][TAG] -------------------------------------------------------------------------------- Time 20.36 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11492 4.18e-05 50_[+2(1.84e-06)]_3_[+3(9.75e-07)]_\ 406 11799 4.79e-08 36_[+2(1.86e-07)]_82_[+1(8.80e-05)]_\ 26_[+1(2.24e-08)]_293 17008 2.37e-07 225_[+2(2.52e-08)]_55_\ [+3(3.76e-07)]_179 21260 2.95e-07 91_[+2(1.17e-06)]_112_\ [+1(7.30e-09)]_46_[+1(5.13e-05)]_188 22667 2.94e-05 142_[+3(8.53e-06)]_293_\ [+1(1.41e-07)]_24 23734 8.14e-07 1_[+2(1.36e-05)]_8_[+3(8.70e-08)]_\ 429_[+1(3.02e-05)] 25104 3.89e-06 122_[+2(3.06e-06)]_155_\ [+1(7.43e-07)]_181 25526 4.73e-05 182_[+1(1.39e-05)]_110_\ [+2(6.61e-07)]_89_[+2(8.35e-06)]_56 25772 1.20e-07 263_[+2(7.76e-06)]_180_\ [+1(7.29e-10)]_15 261293 2.39e-05 119_[+2(5.34e-06)]_109_\ [+3(1.86e-07)]_231 261635 3.01e-11 8_[+3(2.37e-07)]_62_[+2(1.06e-08)]_\ 367_[+1(2.19e-07)]_1 262513 4.13e-09 98_[+2(5.65e-09)]_207_\ [+3(2.29e-06)]_115_[+1(8.44e-06)]_18 263415 4.17e-10 37_[+2(8.03e-07)]_177_\ [+3(2.48e-09)]_223_[+1(4.60e-06)]_1 264672 1.64e-05 230_[+1(2.40e-06)]_83_\ [+3(3.90e-05)]_80_[+2(1.11e-05)]_45 269714 2.75e-10 197_[+2(3.41e-10)]_16_\ [+3(2.11e-05)]_105_[+1(8.17e-07)]_120 28317 3.54e-04 43_[+3(3.86e-06)]_8_[+3(6.07e-05)]_\ 26_[+1(9.76e-06)]_362 30105 6.28e-06 78_[+3(8.70e-08)]_208_\ [+2(1.27e-05)]_173 32223 1.76e-02 425_[+1(1.85e-06)]_54 34379 3.78e-02 201_[+1(3.62e-06)]_278 35372 2.91e-06 5_[+3(1.73e-05)]_231_[+2(1.84e-06)]_\ 167_[+1(4.60e-06)]_10_[+1(5.74e-05)]_4 3579 1.56e-05 16_[+2(7.21e-06)]_142_\ [+3(2.72e-05)]_242_[+1(4.98e-06)]_38 37328 8.84e-04 152_[+3(1.31e-06)]_251_\ [+3(7.47e-05)]_57 37441 4.05e-09 1_[+1(1.97e-07)]_200_[+2(4.23e-06)]_\ 59_[+3(1.28e-07)]_178 3787 1.94e-06 71_[+3(1.51e-05)]_97_[+2(3.06e-06)]_\ 256_[+1(2.02e-06)]_14 39802 3.20e-04 370_[+1(2.50e-05)]_84_\ [+1(1.97e-07)]_4 4830 1.24e-08 163_[+3(2.74e-06)]_78_\ [+2(1.17e-06)]_197_[+1(1.12e-07)] 7942 3.76e-02 365_[+1(1.12e-05)]_114 9238 1.78e-06 99_[+3(6.47e-07)]_143_\ [+1(1.81e-05)]_196_[+1(8.90e-08)] 961 7.73e-04 290_[+3(1.46e-07)]_190 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************