******************************************************************************** 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/202/202.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31879 1.0000 500 32139 1.0000 500 43226 1.0000 500 17967 1.0000 500 13235 1.0000 500 13534 1.0000 500 13309 1.0000 500 13835 1.0000 500 37260 1.0000 500 37556 1.0000 500 14138 1.0000 500 14161 1.0000 500 3334 1.0000 500 32646 1.0000 500 43446 1.0000 500 43487 1.0000 500 9893 1.0000 500 4974 1.0000 500 49210 1.0000 500 49441 1.0000 500 30960 1.0000 500 41091 1.0000 500 43788 1.0000 500 41785 1.0000 500 26035 1.0000 500 44442 1.0000 500 44592 1.0000 500 19122 1.0000 500 34116 1.0000 500 19438 1.0000 500 5424 1.0000 500 45001 1.0000 500 7426 1.0000 500 26925 1.0000 500 45871 1.0000 500 46145 1.0000 500 43504 1.0000 500 40209 1.0000 500 48945 1.0000 500 37093 1.0000 500 45749 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/202/202.seqs.fa -oc motifs/202 -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= 41 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= 20500 N= 41 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.240 G 0.229 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.240 G 0.229 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 20 llr = 239 E-value = 7.9e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2:2132:::91914:a43: pos.-specific C 3:22523:a17:1:a:333 probability G 1612:11::1218:::314 matrix T 5565256a:11117::144 bits 2.1 * * 1.9 ** ** 1.7 ** ** 1.5 ** ** Relative 1.3 ** * ** Entropy 1.1 * *** ***** (17.3 bits) 0.8 * *** ***** 0.6 * ********** 0.4 * * ********** * 0.2 ******************* 0.0 ------------------- Multilevel TGTTCTTTCACAGTCAATT consensus CTACAAC A GAG sequence A GTC CCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 37260 173 1.74e-08 CTACCTGTAC CGTTCATTCACAGACAGTT TGCCTCCCGA 13235 276 9.07e-08 TTTCCAACGC TTTTTTCTCACAGACAGAC CGGATATGGA 46145 216 1.04e-07 AGGATTAAAT GGATCTTTCACAGTCAGTT CGTGTTGTCG 40209 262 1.70e-07 GTCTCGGTTT TGAGCGTTCACAGTCAAAC GACGTAAGGT 31879 121 1.70e-07 GTTCTCCGTC AGCTCTTTCAGAGTCAAAT AAGCAACAAT 45749 139 6.94e-07 GCAGGGCGAT TGATATCTCAAAGACAACT GGGATGACAG 37093 415 7.66e-07 AAAGCTTGGG TTTGCGTTCAAAGTCACCG TGGATGTAGG 44442 80 7.66e-07 GAATCGCCGT CGCTCACTCACAGTCAAGG ATATTCTTCA 41785 28 1.02e-06 AATTGTCACC TGGTATGTCAGAGTCAACG AACGATAAAT 9893 223 1.02e-06 ACATCAGAAA ATTTCTCTCACAATCAGTC AATTGAAAAA 37556 378 1.12e-06 TCGTATTCAT TGTCACTTCACTGTCAGTG GAGAGATAGG 45001 411 1.23e-06 GAGATAGATG TGACTTCTCACAGTCATTT CGAATTTTTC 30960 202 1.47e-06 GTTATTGCTG CTTTTTCTCACACTCACCT TCGGCATTAA 26925 224 2.46e-06 TTACCCTTGC CTTACTTTCTCAGACAAAG TCAAGAGAGA 43504 41 2.67e-06 ACGTTTACGC CGTGACTTCCCAGACAAAG TCGCCATGAT 34116 233 2.67e-06 GTGCGTGTAG ATTGAATTCATAGTCAATG ACAAAAGGCA 19438 449 2.90e-06 GTCAAGCTCG TTTTCTTTCACGTACACCT TACAGCAACA 43226 481 4.96e-06 ACCGCACCGT TGTCCCGTCACATACACAC A 41091 214 7.09e-06 TCTGAAAATG TTCCTCTTCGCAGTCAGCC TTACCATAAG 48945 157 9.27e-06 ATAGCTTCTG ATGAAATTCAGAGTCACTT CCCGGCAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37260 1.7e-08 172_[+1]_309 13235 9.1e-08 275_[+1]_206 46145 1e-07 215_[+1]_266 40209 1.7e-07 261_[+1]_220 31879 1.7e-07 120_[+1]_361 45749 6.9e-07 138_[+1]_343 37093 7.7e-07 414_[+1]_67 44442 7.7e-07 79_[+1]_402 41785 1e-06 27_[+1]_454 9893 1e-06 222_[+1]_259 37556 1.1e-06 377_[+1]_104 45001 1.2e-06 410_[+1]_71 30960 1.5e-06 201_[+1]_280 26925 2.5e-06 223_[+1]_258 43504 2.7e-06 40_[+1]_441 34116 2.7e-06 232_[+1]_249 19438 2.9e-06 448_[+1]_33 43226 5e-06 480_[+1]_1 41091 7.1e-06 213_[+1]_268 48945 9.3e-06 156_[+1]_325 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=20 37260 ( 173) CGTTCATTCACAGACAGTT 1 13235 ( 276) TTTTTTCTCACAGACAGAC 1 46145 ( 216) GGATCTTTCACAGTCAGTT 1 40209 ( 262) TGAGCGTTCACAGTCAAAC 1 31879 ( 121) AGCTCTTTCAGAGTCAAAT 1 45749 ( 139) TGATATCTCAAAGACAACT 1 37093 ( 415) TTTGCGTTCAAAGTCACCG 1 44442 ( 80) CGCTCACTCACAGTCAAGG 1 41785 ( 28) TGGTATGTCAGAGTCAACG 1 9893 ( 223) ATTTCTCTCACAATCAGTC 1 37556 ( 378) TGTCACTTCACTGTCAGTG 1 45001 ( 411) TGACTTCTCACAGTCATTT 1 30960 ( 202) CTTTTTCTCACACTCACCT 1 26925 ( 224) CTTACTTTCTCAGACAAAG 1 43504 ( 41) CGTGACTTCCCAGACAAAG 1 34116 ( 233) ATTGAATTCATAGTCAATG 1 19438 ( 449) TTTTCTTTCACGTACACCT 1 43226 ( 481) TGTCCCGTCACATACACAC 1 41091 ( 214) TTCCTCTTCGCAGTCAGCC 1 48945 ( 157) ATGAAATTCAGAGTCACTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 19762 bayes= 10.1988 E= 7.9e-004 -42 6 -219 93 -1097 -1097 126 78 -42 -68 -120 107 -142 -26 -20 93 16 106 -1097 -39 -42 -26 -120 93 -1097 32 -120 119 -1097 -1097 -1097 193 -1097 206 -1097 -1097 166 -226 -219 -239 -142 155 -61 -239 175 -1097 -219 -239 -242 -226 180 -139 38 -1097 -1097 131 -1097 206 -1097 -1097 190 -1097 -1097 -1097 58 6 39 -239 16 32 -219 41 -1097 6 61 61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 20 E= 7.9e-004 0.200000 0.250000 0.050000 0.500000 0.000000 0.000000 0.550000 0.450000 0.200000 0.150000 0.100000 0.550000 0.100000 0.200000 0.200000 0.500000 0.300000 0.500000 0.000000 0.200000 0.200000 0.200000 0.100000 0.500000 0.000000 0.300000 0.100000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.850000 0.050000 0.050000 0.050000 0.100000 0.700000 0.150000 0.050000 0.900000 0.000000 0.050000 0.050000 0.050000 0.050000 0.800000 0.100000 0.350000 0.000000 0.000000 0.650000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.250000 0.300000 0.050000 0.300000 0.300000 0.050000 0.350000 0.000000 0.250000 0.350000 0.400000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TCA][GT][TA][TCG][CAT][TAC][TC]TCACAG[TA]CA[AGC][TAC][TGC] -------------------------------------------------------------------------------- Time 13.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 40 llr = 317 E-value = 8.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1::::13::::: pos.-specific C 111232:31262 probability G 1:::73::4713 matrix T 7aa8:5775246 bits 2.1 1.9 1.7 ** 1.5 ** Relative 1.3 **** Entropy 1.1 **** * (11.4 bits) 0.8 **** ** ** 0.6 ***** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTTGTTTTGCT consensus CCGACGTTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 32139 358 7.53e-07 CCAATCCATT TTTTGTTTGGTT TCTTCTCAAC 41785 223 1.74e-06 GGGGAACCGC TTTTGTTTTGCC TTTTGCCCCG 43226 270 1.74e-06 CGGTTTCCTC TTTTGGTTGGCG GATTCGGTGC 32646 55 3.49e-06 GGCCGCATCA TTTTCTTTGGTT ACTTCTTCGC 48945 398 6.82e-06 TTGTCAACGT TTTTGGACTGCT ATTAAACATA 46145 47 6.82e-06 CATGCAAGGC TTTTGGATTGTT GAGCGTCAAC 37093 162 7.92e-06 GCTCTTGTAT TTTTGCATTGCT TGTACTATTC 44442 37 1.07e-05 ACTCTGCTCT GTTTGGTTGGCT CACCGTTTTC 5424 184 1.20e-05 GACCAGTGGG TTTTGTACGGTT CGATTGCGAG 43487 381 1.45e-05 GTGGGGATTT GTTTCTTTTGCT AGCTTGGCTC 17967 218 1.58e-05 CGACAAGAAT TTTTGGACTGTT GTCGAGTGAC 31879 8 1.58e-05 GCTCTCG TTTTGTTCGGTC CATCCATGTA 45871 291 2.36e-05 CGGAGTGGCG TTTTCTTCGTCT GATCTACTGT 43504 484 2.61e-05 ACTTGACTTA TTCTGTTTTGCT ACGCC 49210 381 2.61e-05 CATACACTTC CTTTGTTTTTCT CATCCCGGCA 19438 327 3.04e-05 TCATTTCCCG TTTTCGTTTTCG CGATGATCTT 30960 446 3.04e-05 AAGGCACACA TTTTCCTTTGTG TTAACTGTCC 19122 415 5.18e-05 ACTTTTTCAT TTTTGGTTTGCA GCGTGCAAGA 7426 77 6.42e-05 TCAGAGGGGA TTTCGTTCTTCG CGACAAGGAT 26035 64 6.42e-05 GGTTCTATGG CTTTGTTTTCTT GGAGTCGGCA 9893 41 6.42e-05 AAGTGTGGAA TTTTGATTGGTG TAATTATGAC 45749 350 7.01e-05 CGAGTCCCCC TTTTCTATTCTT GAGCGCTGCC 4974 414 8.47e-05 CGCTGGAATC TTTTCTTCGTCC GGACCGAGTC 43788 330 9.49e-05 ATTGGAGCGA TTTCGTTTGCCC ATTTGCTCTA 37260 350 9.49e-05 CAAGAAACGC CTTTGCTCGGCG AAGAACAGAC 34116 488 1.03e-04 GCAGCTGAAA ATTTGTTTTCCT A 41091 124 1.14e-04 TGCACCGTCC TTTTCCTCTTTT TCCCGGTTAG 14138 96 1.14e-04 GGCCATCCAT TTTTCTCTGGCT CGAAAGCTTG 44592 238 1.35e-04 TTTAGAACGG TTTTGTACCGTT GACGAATGTC 49441 127 1.61e-04 GGCAGTGAGC GTTTGGTTGGGT TGAGATTGAC 40209 137 1.73e-04 CATTGAGGTG TCTTGGTTTCCT TCCATCCTTT 26925 375 2.57e-04 GCAAATTACT GTTCCGTTTGCC GAACAAGCTC 43446 466 2.79e-04 TCATGCCATA TTTTGTATATCT ACCTTCGCCA 14161 190 2.98e-04 ATTCACACAG CTTCCGTTGGTG TTGCTGTGGA 45001 82 4.50e-04 AAGAGTACGC TTTCCGTCTGGG TTTGTATAAT 13235 105 5.49e-04 CGGGATATGA CTTTGAACGGTT GACGGTGAAT 3334 369 7.39e-04 GCCCAGTAGT TTTCGCATCGCC AAGGATGTCT 13534 460 7.80e-04 GGTTTACCAC GTTCCTATGCCG CTGCGTATTC 13835 137 8.74e-04 ATCAGGTATC TTCCGCTTTTCG TAAATGTGTA 37556 80 1.03e-03 TCCAGCAAGT ACTTGTTCTGTG TTGAATGGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32139 7.5e-07 357_[+2]_131 41785 1.7e-06 222_[+2]_266 43226 1.7e-06 269_[+2]_219 32646 3.5e-06 54_[+2]_434 48945 6.8e-06 397_[+2]_91 46145 6.8e-06 46_[+2]_442 37093 7.9e-06 161_[+2]_327 44442 1.1e-05 36_[+2]_452 5424 1.2e-05 183_[+2]_305 43487 1.4e-05 380_[+2]_108 17967 1.6e-05 217_[+2]_271 31879 1.6e-05 7_[+2]_481 45871 2.4e-05 290_[+2]_198 43504 2.6e-05 483_[+2]_5 49210 2.6e-05 380_[+2]_108 19438 3e-05 326_[+2]_162 30960 3e-05 445_[+2]_43 19122 5.2e-05 414_[+2]_74 7426 6.4e-05 76_[+2]_412 26035 6.4e-05 63_[+2]_425 9893 6.4e-05 40_[+2]_448 45749 7e-05 349_[+2]_139 4974 8.5e-05 413_[+2]_75 43788 9.5e-05 329_[+2]_159 37260 9.5e-05 349_[+2]_139 34116 0.0001 487_[+2]_1 41091 0.00011 123_[+2]_365 14138 0.00011 95_[+2]_393 44592 0.00014 237_[+2]_251 49441 0.00016 126_[+2]_362 40209 0.00017 136_[+2]_352 26925 0.00026 374_[+2]_114 43446 0.00028 465_[+2]_23 14161 0.0003 189_[+2]_299 45001 0.00045 81_[+2]_407 13235 0.00055 104_[+2]_384 3334 0.00074 368_[+2]_120 13534 0.00078 459_[+2]_29 13835 0.00087 136_[+2]_352 37556 0.001 79_[+2]_409 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=40 32139 ( 358) TTTTGTTTGGTT 1 41785 ( 223) TTTTGTTTTGCC 1 43226 ( 270) TTTTGGTTGGCG 1 32646 ( 55) TTTTCTTTGGTT 1 48945 ( 398) TTTTGGACTGCT 1 46145 ( 47) TTTTGGATTGTT 1 37093 ( 162) TTTTGCATTGCT 1 44442 ( 37) GTTTGGTTGGCT 1 5424 ( 184) TTTTGTACGGTT 1 43487 ( 381) GTTTCTTTTGCT 1 17967 ( 218) TTTTGGACTGTT 1 31879 ( 8) TTTTGTTCGGTC 1 45871 ( 291) TTTTCTTCGTCT 1 43504 ( 484) TTCTGTTTTGCT 1 49210 ( 381) CTTTGTTTTTCT 1 19438 ( 327) TTTTCGTTTTCG 1 30960 ( 446) TTTTCCTTTGTG 1 19122 ( 415) TTTTGGTTTGCA 1 7426 ( 77) TTTCGTTCTTCG 1 26035 ( 64) CTTTGTTTTCTT 1 9893 ( 41) TTTTGATTGGTG 1 45749 ( 350) TTTTCTATTCTT 1 4974 ( 414) TTTTCTTCGTCC 1 43788 ( 330) TTTCGTTTGCCC 1 37260 ( 350) CTTTGCTCGGCG 1 34116 ( 488) ATTTGTTTTCCT 1 41091 ( 124) TTTTCCTCTTTT 1 14138 ( 96) TTTTCTCTGGCT 1 44592 ( 238) TTTTGTACCGTT 1 49441 ( 127) GTTTGGTTGGGT 1 40209 ( 137) TCTTGGTTTCCT 1 26925 ( 375) GTTCCGTTTGCC 1 43446 ( 466) TTTTGTATATCT 1 14161 ( 190) CTTCCGTTGGTG 1 45001 ( 82) TTTCCGTCTGGG 1 13235 ( 105) CTTTGAACGGTT 1 3334 ( 369) TTTCGCATCGCC 1 13534 ( 460) GTTCCTATGCCG 1 13835 ( 137) TTCCGCTTTTCG 1 37556 ( 80) ACTTGTTCTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 20049 bayes= 9.21843 E= 8.4e-001 -242 -94 -88 141 -1197 -226 -1197 185 -1197 -226 -1197 185 -1197 -26 -1197 161 -1197 44 156 -1197 -242 -68 39 93 4 -326 -1197 141 -1197 44 -1197 136 -342 -226 80 100 -1197 -68 150 -39 -1197 126 -220 51 -342 -68 26 107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 40 E= 8.4e-001 0.050000 0.125000 0.125000 0.700000 0.000000 0.050000 0.000000 0.950000 0.000000 0.050000 0.000000 0.950000 0.000000 0.200000 0.000000 0.800000 0.000000 0.325000 0.675000 0.000000 0.050000 0.150000 0.300000 0.500000 0.275000 0.025000 0.000000 0.700000 0.000000 0.325000 0.000000 0.675000 0.025000 0.050000 0.400000 0.525000 0.000000 0.150000 0.650000 0.200000 0.000000 0.575000 0.050000 0.375000 0.025000 0.150000 0.275000 0.550000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TTT[TC][GC][TG][TA][TC][TG][GT][CT][TG] -------------------------------------------------------------------------------- Time 25.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 16 llr = 189 E-value = 2.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:59:3:169832863 pos.-specific C 832:a::1:11122:6 probability G 1131::a:3:163:41 matrix T 16:::7:91:1:3::: bits 2.1 * * 1.9 * * 1.7 * * 1.5 ** * * Relative 1.3 ** ** * * Entropy 1.1 ***** * ** (17.1 bits) 0.8 * ********* *** 0.6 ** ********* *** 0.4 ************ *** 0.2 ************ *** 0.0 ---------------- Multilevel CTAACTGTAAAGGAAC consensus CG A G AT GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 41091 247 7.50e-09 CATAAGTGAC CTAACTGTAAAGTAAA AAGAATAAAT 19438 372 4.44e-08 CCAAGAAAAC CTGACAGTAAAGGAAA ACAAGAACTA 19122 299 9.89e-08 ACCTTGTTAG CTGACTGTGAAATAGC TTTCGGCGTC 9893 199 1.62e-07 ACTACATTAC CTAACTGTAATGTAAC ATCAGAAAAT 34116 104 3.22e-07 ACGATTCGGT CGCACTGTGAAGCAAC CCGATTACAC 26035 388 3.60e-07 AAACTTTGTG CTAACTGTAAAATCAA TCAAACGGCT 49441 406 8.23e-07 AGCACCGACA CCAACTGTACAGAAAC GGGCACGAAA 43226 131 1.58e-06 ACACAGAACA CGAACAGTAAAGGCGA AACTTACTGT 17967 426 1.73e-06 CACACGAATA CTAACTGTAAGCAAAC ATGTCCGGAA 32139 147 2.42e-06 AATTGCTCTA ATGACAGTGAAGCAGA AGTTACAAGA 44592 257 2.86e-06 GTTGACGAAT GTCGCTGTAAAGGAGC TCGTTTCTTG 43487 57 5.27e-06 GTTCTTCTCT ACCACTGCAAAGGAAC AATGCTTTGT 45001 56 5.66e-06 GGGAGCGGGG TTGACTGTGAACAAGC AAGAGTACGC 43446 236 6.98e-06 TGTGGGGAAG CCAGCTGTAAAACAAG ACCCGATCTG 43504 305 8.01e-06 ATCACTACTG CCAACAGTTACGTAAC CGCAATATAA 32646 180 1.11e-05 TTGATGTATC CTGACAGAGAAAGCGC ATAATAAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41091 7.5e-09 246_[+3]_238 19438 4.4e-08 371_[+3]_113 19122 9.9e-08 298_[+3]_186 9893 1.6e-07 198_[+3]_286 34116 3.2e-07 103_[+3]_381 26035 3.6e-07 387_[+3]_97 49441 8.2e-07 405_[+3]_79 43226 1.6e-06 130_[+3]_354 17967 1.7e-06 425_[+3]_59 32139 2.4e-06 146_[+3]_338 44592 2.9e-06 256_[+3]_228 43487 5.3e-06 56_[+3]_428 45001 5.7e-06 55_[+3]_429 43446 7e-06 235_[+3]_249 43504 8e-06 304_[+3]_180 32646 1.1e-05 179_[+3]_305 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=16 41091 ( 247) CTAACTGTAAAGTAAA 1 19438 ( 372) CTGACAGTAAAGGAAA 1 19122 ( 299) CTGACTGTGAAATAGC 1 9893 ( 199) CTAACTGTAATGTAAC 1 34116 ( 104) CGCACTGTGAAGCAAC 1 26035 ( 388) CTAACTGTAAAATCAA 1 49441 ( 406) CCAACTGTACAGAAAC 1 43226 ( 131) CGAACAGTAAAGGCGA 1 17967 ( 426) CTAACTGTAAGCAAAC 1 32139 ( 147) ATGACAGTGAAGCAGA 1 44592 ( 257) GTCGCTGTAAAGGAGC 1 43487 ( 57) ACCACTGCAAAGGAAC 1 45001 ( 56) TTGACTGTGAACAAGC 1 43446 ( 236) CCAGCTGTAAAACAAG 1 43504 ( 305) CCAACAGTTACGTAAC 1 32646 ( 180) CTGACAGAGAAAGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 19885 bayes= 11.0157 E= 2.0e+001 -110 164 -187 -207 -1064 6 -87 125 90 -35 45 -1064 170 -1064 -87 -1064 -1064 206 -1064 -1064 22 -1064 -1064 139 -1064 -1064 212 -1064 -210 -194 -1064 174 122 -1064 45 -207 180 -194 -1064 -1064 160 -194 -187 -207 -10 -94 145 -1064 -52 -35 45 25 160 -35 -1064 -1064 122 -1064 71 -1064 22 138 -187 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 2.0e+001 0.125000 0.750000 0.062500 0.062500 0.000000 0.250000 0.125000 0.625000 0.500000 0.187500 0.312500 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.312500 0.000000 0.000000 0.687500 0.000000 0.000000 1.000000 0.000000 0.062500 0.062500 0.000000 0.875000 0.625000 0.000000 0.312500 0.062500 0.937500 0.062500 0.000000 0.000000 0.812500 0.062500 0.062500 0.062500 0.250000 0.125000 0.625000 0.000000 0.187500 0.187500 0.312500 0.312500 0.812500 0.187500 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.312500 0.625000 0.062500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TC][AG]AC[TA]GT[AG]AA[GA][GT]A[AG][CA] -------------------------------------------------------------------------------- Time 38.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31879 6.16e-05 7_[+2(1.58e-05)]_101_[+1(1.70e-07)]_\ 361 32139 2.08e-05 146_[+3(2.42e-06)]_195_\ [+2(7.53e-07)]_131 43226 3.53e-07 40_[+2(9.49e-05)]_78_[+3(1.58e-06)]_\ 123_[+2(1.74e-06)]_199_[+1(4.96e-06)]_1 17967 2.63e-04 217_[+2(1.58e-05)]_196_\ [+3(1.73e-06)]_59 13235 5.62e-04 275_[+1(9.07e-08)]_206 13534 5.34e-01 500 13309 7.70e-01 500 13835 5.43e-01 500 37260 3.75e-05 12_[+1(7.56e-05)]_141_\ [+1(1.74e-08)]_158_[+2(9.49e-05)]_139 37556 8.56e-03 377_[+1(1.12e-06)]_104 14138 8.42e-02 500 14161 2.55e-01 500 3334 3.35e-01 500 32646 5.91e-04 54_[+2(3.49e-06)]_113_\ [+3(1.11e-05)]_305 43446 6.48e-03 235_[+3(6.98e-06)]_249 43487 8.30e-04 56_[+3(5.27e-06)]_308_\ [+2(1.45e-05)]_108 9893 2.77e-07 40_[+2(6.42e-05)]_146_\ [+3(1.62e-07)]_8_[+1(1.02e-06)]_259 4974 1.37e-01 413_[+2(8.47e-05)]_75 49210 3.53e-02 380_[+2(2.61e-05)]_108 49441 1.76e-03 405_[+3(8.23e-07)]_79 30960 5.44e-04 201_[+1(1.47e-06)]_225_\ [+2(3.04e-05)]_43 41091 1.65e-07 213_[+1(7.09e-06)]_14_\ [+3(7.50e-09)]_238 43788 9.20e-02 329_[+2(9.49e-05)]_159 41785 4.47e-05 27_[+1(1.02e-06)]_176_\ [+2(1.74e-06)]_266 26035 3.62e-04 63_[+2(6.42e-05)]_312_\ [+3(3.60e-07)]_97 44442 1.32e-05 5_[+3(9.72e-05)]_15_[+2(1.07e-05)]_\ 31_[+1(7.66e-07)]_402 44592 1.87e-03 256_[+3(2.86e-06)]_228 19122 9.75e-05 298_[+3(9.89e-08)]_100_\ [+2(5.18e-05)]_74 34116 1.86e-06 103_[+3(3.22e-07)]_113_\ [+1(2.67e-06)]_249 19438 1.13e-07 326_[+2(3.04e-05)]_33_\ [+3(4.44e-08)]_61_[+1(2.90e-06)]_33 5424 1.63e-02 183_[+2(1.20e-05)]_305 45001 4.10e-05 55_[+3(5.66e-06)]_339_\ [+1(1.23e-06)]_71 7426 9.69e-02 76_[+2(6.42e-05)]_412 26925 3.64e-03 223_[+1(2.46e-06)]_258 45871 3.49e-02 290_[+2(2.36e-05)]_198 46145 4.69e-06 46_[+2(6.82e-06)]_157_\ [+1(1.04e-07)]_266 43504 9.80e-06 40_[+1(2.67e-06)]_245_\ [+3(8.01e-06)]_163_[+2(2.61e-05)]_5 40209 6.68e-05 261_[+1(1.70e-07)]_220 48945 5.34e-04 156_[+1(9.27e-06)]_222_\ [+2(6.82e-06)]_91 37093 1.43e-04 161_[+2(7.92e-06)]_241_\ [+1(7.66e-07)]_67 45749 1.94e-04 138_[+1(6.94e-07)]_192_\ [+2(7.01e-05)]_139 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************