******************************************************************************** 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/424/424.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10899 1.0000 500 15093 1.0000 500 20984 1.0000 500 21136 1.0000 500 22395 1.0000 500 22864 1.0000 500 23047 1.0000 500 2320 1.0000 500 23779 1.0000 500 23827 1.0000 500 23867 1.0000 500 23987 1.0000 500 24460 1.0000 500 24534 1.0000 500 25495 1.0000 500 261124 1.0000 500 268564 1.0000 500 269127 1.0000 500 28651 1.0000 500 32067 1.0000 500 34900 1.0000 500 36291 1.0000 500 36297 1.0000 500 38360 1.0000 500 41632 1.0000 500 7752 1.0000 500 9173 1.0000 500 9714 1.0000 500 bd410 1.0000 500 bd415 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/424/424.seqs.fa -oc motifs/424 -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= 30 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= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.240 G 0.229 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.240 G 0.229 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 25 llr = 244 E-value = 1.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :84172162294424: pos.-specific C :::::3::5::32:32 probability G a239237337124818 matrix T ::2:1221:1:1::2: bits 2.1 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 ** * * * * Entropy 1.1 ** * ** * * (14.1 bits) 0.9 ** * * ** * * 0.6 ** ** ** ** * * 0.4 ***** ***** ** * 0.2 ***** ***** **** 0.0 ---------------- Multilevel GAAGAGGACGAAAGAG consensus GG GC GGA CGAC sequence T A A GC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 7752 108 1.60e-08 GGATCCGATA GAGGACGACGAGAGCG AGCAGGCCGG 34900 147 2.96e-08 CGGCCATGGC GAGGAGGGCGAAGGCG GTGGTCTTCA 23867 166 4.95e-07 TTGGTGACGA GAGGGAGAGGAAGGAG AGGAGAGATA 28651 311 5.75e-07 GCGTGTATGC GAGGAAGGAGACGGAG GGAAGAGGTA 24534 346 6.67e-07 GTGTTAGGTT GAAGACTACGACAGTG TATCGGTTGA bd410 432 1.76e-06 CTTGTTCTCA GAGGATGAGGATGGTG GTGGTAGTGG 15093 95 3.21e-06 TGCAAGTAAA GAAGATGAAGACGAAG CGAATGTCGA 41632 90 3.60e-06 TTCTGGCATG GGAGGGGAGGAGCGAG TTGAAATTGG 9714 251 5.01e-06 CAAGGCCAAC GAGGGAGGCGAAGACG CCGGGGTGGT 23827 32 6.19e-06 GAATCATAAT GAAGAGGTCGGCAGCG GTTGAGAAGT 23047 352 6.19e-06 ATCGGGCGGC GGAGGAGGGGAAAGTG TTGATTCGAG 22864 50 1.02e-05 TGGAACAATC GATGTGTACGACGGTG CCGCAGACGC 268564 249 1.35e-05 TGGTCGAGGG GGTGAGTACGAAAGGG GAAAACGTTA 23987 2 1.62e-05 C GGAGAGGAGAAGAACG AGGCTATTGG 10899 385 1.62e-05 ACAAGTCTTG GAAGAGTTCGATCGAG AACAAGAAAC 36291 188 1.93e-05 GACCATATTC GATAGCGGCGACAGCG GCAAGTGACT 23779 331 3.15e-05 ATCAAGTTTA GAAGATGAATAAAGCC ACAGCGTTTT 9173 379 3.96e-05 CCGAATTTCG GAGGAGGAAAACAAAC CAAAAAGCGT 24460 71 4.58e-05 ATGACGATGA CATGACGAGGAGGGGG GTCGGTCGGG 22395 137 4.58e-05 CAGAACTCAA GAGGAAAGAGAACAAG CCCTTGCCTT bd415 17 4.92e-05 GAGAGTTCTT GAAGAAGGCTGACGAG CTCATCAATG 269127 289 6.49e-05 TGCAGTACAC GAAGACAACAAGCGTC ATAGTTCCGT 36297 40 7.40e-05 TGACGCGGTA GATGTTGTGAAGAGAG GGCGATATGC 32067 293 7.89e-05 GCGACTCTTG GGAAACAAAGAAGGCG GGAACAACAA 20984 258 8.95e-05 AGTTTTTGCC GATGTCGACAATAGTC GGACATGGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7752 1.6e-08 107_[+1]_377 34900 3e-08 146_[+1]_338 23867 4.9e-07 165_[+1]_319 28651 5.7e-07 310_[+1]_174 24534 6.7e-07 345_[+1]_139 bd410 1.8e-06 431_[+1]_53 15093 3.2e-06 94_[+1]_390 41632 3.6e-06 89_[+1]_395 9714 5e-06 250_[+1]_234 23827 6.2e-06 31_[+1]_453 23047 6.2e-06 351_[+1]_133 22864 1e-05 49_[+1]_435 268564 1.4e-05 248_[+1]_236 23987 1.6e-05 1_[+1]_483 10899 1.6e-05 384_[+1]_100 36291 1.9e-05 187_[+1]_297 23779 3.1e-05 330_[+1]_154 9173 4e-05 378_[+1]_106 24460 4.6e-05 70_[+1]_414 22395 4.6e-05 136_[+1]_348 bd415 4.9e-05 16_[+1]_468 269127 6.5e-05 288_[+1]_196 36297 7.4e-05 39_[+1]_445 32067 7.9e-05 292_[+1]_192 20984 8.9e-05 257_[+1]_227 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=25 7752 ( 108) GAGGACGACGAGAGCG 1 34900 ( 147) GAGGAGGGCGAAGGCG 1 23867 ( 166) GAGGGAGAGGAAGGAG 1 28651 ( 311) GAGGAAGGAGACGGAG 1 24534 ( 346) GAAGACTACGACAGTG 1 bd410 ( 432) GAGGATGAGGATGGTG 1 15093 ( 95) GAAGATGAAGACGAAG 1 41632 ( 90) GGAGGGGAGGAGCGAG 1 9714 ( 251) GAGGGAGGCGAAGACG 1 23827 ( 32) GAAGAGGTCGGCAGCG 1 23047 ( 352) GGAGGAGGGGAAAGTG 1 22864 ( 50) GATGTGTACGACGGTG 1 268564 ( 249) GGTGAGTACGAAAGGG 1 23987 ( 2) GGAGAGGAGAAGAACG 1 10899 ( 385) GAAGAGTTCGATCGAG 1 36291 ( 188) GATAGCGGCGACAGCG 1 23779 ( 331) GAAGATGAATAAAGCC 1 9173 ( 379) GAGGAGGAAAACAAAC 1 24460 ( 71) CATGACGAGGAGGGGG 1 22395 ( 137) GAGGAAAGAGAACAAG 1 bd415 ( 17) GAAGAAGGCTGACGAG 1 269127 ( 289) GAAGACAACAAGCGTC 1 36297 ( 40) GATGTTGTGAAGAGAG 1 32067 ( 293) GGAAACAAAGAAGGCG 1 20984 ( 258) GATGTCGACAATAGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14550 bayes= 9.67316 E= 1.2e-002 -1129 -258 207 -1129 155 -1129 -20 -1129 69 -1129 48 -10 -177 -1129 201 -1129 132 -1129 -20 -110 -19 22 48 -69 -119 -1129 165 -69 114 -1129 29 -110 -19 100 29 -1129 -45 -1129 165 -169 175 -1129 -152 -1129 40 22 7 -110 69 -26 65 -1129 -45 -1129 180 -1129 40 41 -152 -10 -1129 -59 187 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 25 E= 1.2e-002 0.000000 0.040000 0.960000 0.000000 0.800000 0.000000 0.200000 0.000000 0.440000 0.000000 0.320000 0.240000 0.080000 0.000000 0.920000 0.000000 0.680000 0.000000 0.200000 0.120000 0.240000 0.280000 0.320000 0.160000 0.120000 0.000000 0.720000 0.160000 0.600000 0.000000 0.280000 0.120000 0.240000 0.480000 0.280000 0.000000 0.200000 0.000000 0.720000 0.080000 0.920000 0.000000 0.080000 0.000000 0.360000 0.280000 0.240000 0.120000 0.440000 0.200000 0.360000 0.000000 0.200000 0.000000 0.800000 0.000000 0.360000 0.320000 0.080000 0.240000 0.000000 0.160000 0.840000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AG][AGT]G[AG][GCA]G[AG][CGA][GA]A[ACG][AGC][GA][ACT]G -------------------------------------------------------------------------------- Time 7.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 13 llr = 182 E-value = 7.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 6223:5:::2:::::::2::: pos.-specific C 3555a:28238229:841565 probability G 11:1:1:26::5::8:42::5 matrix T :222:58:252381222554: bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * * Relative 1.3 * ** * **** Entropy 1.1 * ** * **** *** (20.2 bits) 0.9 * *** * **** *** 0.6 * * ************ *** 0.4 * * ************* *** 0.2 ********************* 0.0 --------------------- Multilevel ACCCCATCGTCGTCGCCTCCG consensus CAAA T CC T T GATTC sequence TT TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 34900 423 7.48e-10 CATTTTGTCT AATCCATCGTCGTCGCCGCCG TCCATCACAG 2320 344 7.48e-10 CTGCGCCCCT ACCACTTCCTCGTCGCCGTCG CAAAGAAAAG 21136 135 4.32e-09 AGCACCAGAC AACCCTTCGTCTCCGCCTCCC AATAGCGAAT 22395 219 2.62e-08 CATACCGTTC ACTCCATCGACCTCGCCATCG CCTCTGCTTG 36291 388 3.68e-08 CCCCTTGATG CCACCATCGCTTTCGCGTCCC TACGCTTTCA 268564 434 1.78e-07 AAGCTCGCCT CCCTCATCTCCCTCGCGATCG CAACGGCCAA bd415 199 2.72e-07 AAAGGTCTTC CTCGCATCGTCGCCTCGTCTG TGTTGGAAAC 38360 144 4.04e-07 ACGCTCCCCC CCCCCGCCGTCGTCGTGGTTG ATCACAATTC 7752 350 5.44e-07 ATGATCTAAC ATCTCTTGCCCGTCGTCTTCC AAAGCATCAA 36297 178 5.84e-07 CACAAGCTAT AAACCACCGACGTCTCTTCTC TCGAGCACAG 32067 269 7.71e-07 GTGTGAGTCC ACTACTTGGTCTTTGCGACTC TTGGGAAACA 269127 380 1.21e-06 TCATGTTGTG AGAACTTCCTCGTCTCTCTCC GACATCGTTC 9714 132 1.62e-06 TAGTGTGATG GTCACTTCTCTTTCGCTTCTG AGATCCCATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34900 7.5e-10 422_[+2]_57 2320 7.5e-10 343_[+2]_136 21136 4.3e-09 134_[+2]_345 22395 2.6e-08 218_[+2]_261 36291 3.7e-08 387_[+2]_92 268564 1.8e-07 433_[+2]_46 bd415 2.7e-07 198_[+2]_281 38360 4e-07 143_[+2]_336 7752 5.4e-07 349_[+2]_130 36297 5.8e-07 177_[+2]_302 32067 7.7e-07 268_[+2]_211 269127 1.2e-06 379_[+2]_100 9714 1.6e-06 131_[+2]_348 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=13 34900 ( 423) AATCCATCGTCGTCGCCGCCG 1 2320 ( 344) ACCACTTCCTCGTCGCCGTCG 1 21136 ( 135) AACCCTTCGTCTCCGCCTCCC 1 22395 ( 219) ACTCCATCGACCTCGCCATCG 1 36291 ( 388) CCACCATCGCTTTCGCGTCCC 1 268564 ( 434) CCCTCATCTCCCTCGCGATCG 1 bd415 ( 199) CTCGCATCGTCGCCTCGTCTG 1 38360 ( 144) CCCCCGCCGTCGTCGTGGTTG 1 7752 ( 350) ATCTCTTGCCCGTCGTCTTCC 1 36297 ( 178) AAACCACCGACGTCTCTTCTC 1 32067 ( 269) ACTACTTGGTCTTTGCGACTC 1 269127 ( 380) AGAACTTCCTCGTCTCTCTCC 1 9714 ( 132) GTCACTTCTCTTTCGCTTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 11.2771 E= 7.4e-001 117 36 -157 -1035 -24 94 -157 -16 -24 116 -1035 -16 17 94 -157 -74 -1035 206 -1035 -1035 76 -1035 -157 84 -1035 -64 -1035 171 -1035 182 -57 -1035 -1035 -6 143 -74 -83 36 -1035 106 -1035 182 -1035 -74 -1035 -64 123 26 -1035 -64 -1035 171 -1035 194 -1035 -174 -1035 -1035 175 -16 -1035 182 -1035 -74 -1035 68 75 -16 -24 -164 1 84 -1035 116 -1035 84 -1035 136 -1035 58 -1035 94 123 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 7.4e-001 0.615385 0.307692 0.076923 0.000000 0.230769 0.461538 0.076923 0.230769 0.230769 0.538462 0.000000 0.230769 0.307692 0.461538 0.076923 0.153846 0.000000 1.000000 0.000000 0.000000 0.461538 0.000000 0.076923 0.461538 0.000000 0.153846 0.000000 0.846154 0.000000 0.846154 0.153846 0.000000 0.000000 0.230769 0.615385 0.153846 0.153846 0.307692 0.000000 0.538462 0.000000 0.846154 0.000000 0.153846 0.000000 0.153846 0.538462 0.307692 0.000000 0.153846 0.000000 0.846154 0.000000 0.923077 0.000000 0.076923 0.000000 0.000000 0.769231 0.230769 0.000000 0.846154 0.000000 0.153846 0.000000 0.384615 0.384615 0.230769 0.230769 0.076923 0.230769 0.461538 0.000000 0.538462 0.000000 0.461538 0.000000 0.615385 0.000000 0.384615 0.000000 0.461538 0.538462 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC][CAT][CAT][CA]C[AT]TC[GC][TC]C[GT]TC[GT]C[CGT][TAG][CT][CT][GC] -------------------------------------------------------------------------------- Time 15.02 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 14 llr = 182 E-value = 2.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5:::::12414::4:31:: pos.-specific C 1:6:::2:46::8:4:21: probability G :138::5422:111:41:9 matrix T 4912aa1411691563591 bits 2.1 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 ATCGTTGGACTTCTTGTTG consensus T GT CTCGA ACAC sequence AG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 34900 401 3.01e-10 CAAGTGATCC ATCGTTGGACTTCATTTTG TCTAATCCAT 24460 5 5.74e-09 AAGC ATCGTTGTACATCATGGTG CTCGTCTCGT 28651 35 3.96e-08 GAGCAGGGTG ATGTTTGTGCTTCTTTTTG CCCTGTCTGC 269127 72 1.43e-07 GCGGTGAGGA TTGTTTCGACTTCGTGTTG GTGGGCATAA 23867 421 1.43e-07 TTCAACTTGA TGCGTTCGACTTCTTGCTG CCGACGGACG 38360 388 1.95e-07 AATTTTGATG ATGGTTGGCGTTGTTGGTG TGGGGATCGG 10899 427 2.15e-07 GGAAATCGGT ATCTTTTGCCATCACATTG CAGAACAAAA 32067 416 3.16e-07 CTTTCTTTCA TTGGTTATCGATCTCATTG ACAAGGGTTG 23047 294 8.78e-07 CGTTTGTTGG TTCGTTTTCTATCTCAATG AACCACATCG 20984 12 8.78e-07 CTACCTTCTG ATTGTTGTGATTCATTCTG GACCATTTGA 36297 4 1.58e-06 GGC ATCGTTAATGTTGTTGTTG CTGGACATGA 9714 422 4.31e-06 CGCATATCCG TTTGTTGACTATCTTGACG TTCTTCCTCC 25495 52 4.81e-06 GTTGTGTAAC CTCGTTCGGCATTGCATTG TAATGGCAAC 15093 309 5.08e-06 TAGTGCCAAG TTCGTTGAACTGCACTCTT GGAAGTAGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34900 3e-10 400_[+3]_81 24460 5.7e-09 4_[+3]_477 28651 4e-08 34_[+3]_447 269127 1.4e-07 71_[+3]_410 23867 1.4e-07 420_[+3]_61 38360 1.9e-07 387_[+3]_94 10899 2.2e-07 426_[+3]_55 32067 3.2e-07 415_[+3]_66 23047 8.8e-07 293_[+3]_188 20984 8.8e-07 11_[+3]_470 36297 1.6e-06 3_[+3]_478 9714 4.3e-06 421_[+3]_60 25495 4.8e-06 51_[+3]_430 15093 5.1e-06 308_[+3]_173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=14 34900 ( 401) ATCGTTGGACTTCATTTTG 1 24460 ( 5) ATCGTTGTACATCATGGTG 1 28651 ( 35) ATGTTTGTGCTTCTTTTTG 1 269127 ( 72) TTGTTTCGACTTCGTGTTG 1 23867 ( 421) TGCGTTCGACTTCTTGCTG 1 38360 ( 388) ATGGTTGGCGTTGTTGGTG 1 10899 ( 427) ATCTTTTGCCATCACATTG 1 32067 ( 416) TTGGTTATCGATCTCATTG 1 23047 ( 294) TTCGTTTTCTATCTCAATG 1 20984 ( 12) ATTGTTGTGATTCATTCTG 1 36297 ( 4) ATCGTTAATGTTGTTGTTG 1 9714 ( 422) TTTGTTGACTATCTTGACG 1 25495 ( 52) CTCGTTCGGCATTGCATTG 1 15093 ( 309) TTCGTTGAACTGCACTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 14460 bayes= 10.6172 E= 2.6e-001 87 -175 -1045 73 -1045 -1045 -168 185 -1045 125 32 -85 -1045 -1045 178 -27 -1045 -1045 -1045 195 -1045 -1045 -1045 195 -93 -16 113 -85 -35 -1045 90 47 39 57 -10 -185 -193 125 -10 -85 65 -1045 -1045 115 -1045 -1045 -168 185 -1045 171 -68 -185 39 -1045 -68 96 -1045 57 -1045 132 7 -1045 90 15 -93 -16 -68 96 -1045 -175 -1045 185 -1045 -1045 202 -185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 14 E= 2.6e-001 0.500000 0.071429 0.000000 0.428571 0.000000 0.000000 0.071429 0.928571 0.000000 0.571429 0.285714 0.142857 0.000000 0.000000 0.785714 0.214286 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.214286 0.500000 0.142857 0.214286 0.000000 0.428571 0.357143 0.357143 0.357143 0.214286 0.071429 0.071429 0.571429 0.214286 0.142857 0.428571 0.000000 0.000000 0.571429 0.000000 0.000000 0.071429 0.928571 0.000000 0.785714 0.142857 0.071429 0.357143 0.000000 0.142857 0.500000 0.000000 0.357143 0.000000 0.642857 0.285714 0.000000 0.428571 0.285714 0.142857 0.214286 0.142857 0.500000 0.000000 0.071429 0.000000 0.928571 0.000000 0.000000 0.928571 0.071429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AT]T[CG][GT]TT[GC][GTA][ACG][CG][TA]TC[TA][TC][GAT][TC]TG -------------------------------------------------------------------------------- Time 22.29 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10899 3.96e-05 384_[+1(1.62e-05)]_26_\ [+3(2.15e-07)]_55 15093 3.08e-05 94_[+1(3.21e-06)]_108_\ [+1(4.26e-05)]_74_[+3(5.08e-06)]_173 20984 4.47e-04 11_[+3(8.78e-07)]_227_\ [+1(8.95e-05)]_227 21136 2.01e-05 134_[+2(4.32e-09)]_18_\ [+2(9.61e-05)]_306 22395 5.23e-06 136_[+1(4.58e-05)]_66_\ [+2(2.62e-08)]_261 22864 3.48e-03 49_[+1(1.02e-05)]_435 23047 1.33e-04 293_[+3(8.78e-07)]_39_\ [+1(6.19e-06)]_133 2320 1.92e-05 343_[+2(7.48e-10)]_136 23779 4.26e-02 330_[+1(3.15e-05)]_154 23827 8.95e-03 31_[+1(6.19e-06)]_453 23867 2.61e-06 79_[+1(6.19e-06)]_70_[+1(4.95e-07)]_\ 239_[+3(1.43e-07)]_61 23987 6.92e-03 1_[+1(1.62e-05)]_483 24460 7.63e-06 4_[+3(5.74e-09)]_47_[+1(4.58e-05)]_\ 414 24534 8.61e-04 345_[+1(6.67e-07)]_8_[+1(3.67e-05)]_\ 115 25495 1.58e-02 51_[+3(4.81e-06)]_430 261124 5.05e-01 500 268564 2.22e-05 248_[+1(1.35e-05)]_169_\ [+2(1.78e-07)]_46 269127 2.87e-07 71_[+3(1.43e-07)]_198_\ [+1(6.49e-05)]_75_[+2(1.21e-06)]_100 28651 1.40e-07 16_[+1(7.40e-05)]_2_[+3(3.96e-08)]_\ 257_[+1(5.75e-07)]_174 32067 4.67e-07 162_[+2(9.01e-05)]_85_\ [+2(7.71e-07)]_3_[+1(7.89e-05)]_107_[+3(3.16e-07)]_66 34900 6.85e-16 146_[+1(2.96e-08)]_238_\ [+3(3.01e-10)]_3_[+2(7.48e-10)]_57 36291 2.02e-05 187_[+1(1.93e-05)]_116_\ [+2(8.19e-06)]_47_[+2(3.68e-08)]_92 36297 1.47e-06 3_[+3(1.58e-06)]_17_[+1(7.40e-05)]_\ 122_[+2(5.84e-07)]_29_[+2(6.42e-05)]_252 38360 1.12e-06 143_[+2(4.04e-07)]_50_\ [+2(1.13e-05)]_152_[+3(1.95e-07)]_94 41632 1.06e-02 89_[+1(3.60e-06)]_395 7752 3.64e-07 107_[+1(1.60e-08)]_226_\ [+2(5.44e-07)]_130 9173 2.26e-02 378_[+1(3.96e-05)]_106 9714 8.12e-07 131_[+2(1.62e-06)]_98_\ [+1(5.01e-06)]_155_[+3(4.31e-06)]_60 bd410 7.31e-03 431_[+1(1.76e-06)]_53 bd415 2.52e-04 16_[+1(4.92e-05)]_166_\ [+2(2.72e-07)]_281 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************