******************************************************************************** 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/82/82.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10002 1.0000 500 10156 1.0000 500 10434 1.0000 500 10832 1.0000 500 1111 1.0000 500 11186 1.0000 500 11559 1.0000 500 11643 1.0000 500 11918 1.0000 500 11958 1.0000 500 1224 1.0000 500 1393 1.0000 500 1422 1.0000 500 14707 1.0000 500 15138 1.0000 500 15226 1.0000 500 1622 1.0000 500 19793 1.0000 500 20673 1.0000 500 20798 1.0000 500 20903 1.0000 500 21094 1.0000 500 22301 1.0000 500 2267 1.0000 500 23012 1.0000 500 23028 1.0000 500 23064 1.0000 500 23522 1.0000 500 2376 1.0000 500 24220 1.0000 500 24304 1.0000 500 25898 1.0000 500 25910 1.0000 500 25917 1.0000 500 260808 1.0000 500 261327 1.0000 500 261826 1.0000 500 262006 1.0000 500 262009 1.0000 500 262102 1.0000 500 263366 1.0000 500 263798 1.0000 500 268117 1.0000 500 268221 1.0000 500 268247 1.0000 500 269422 1.0000 500 3124 1.0000 500 31569 1.0000 500 32555 1.0000 500 32661 1.0000 500 33513 1.0000 500 33794 1.0000 500 33979 1.0000 500 34210 1.0000 500 35310 1.0000 500 35387 1.0000 500 35968 1.0000 500 36441 1.0000 500 36753 1.0000 500 36788 1.0000 500 370 1.0000 500 37398 1.0000 500 37810 1.0000 500 4041 1.0000 500 4170 1.0000 500 4214 1.0000 500 4217 1.0000 500 42365 1.0000 500 4607 1.0000 500 4688 1.0000 500 4729 1.0000 500 4808 1.0000 500 5009 1.0000 500 5263 1.0000 500 5431 1.0000 500 5662 1.0000 500 5867 1.0000 500 6356 1.0000 500 6586 1.0000 500 6699 1.0000 500 7091 1.0000 500 7092 1.0000 500 7100 1.0000 500 7206 1.0000 500 7586 1.0000 500 8031 1.0000 500 8522 1.0000 500 8536 1.0000 500 8829 1.0000 500 9101 1.0000 500 9684 1.0000 500 9991 1.0000 500 9992 1.0000 500 9993 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/82/82.seqs.fa -oc motifs/82 -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= 94 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= 47000 N= 94 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.236 G 0.236 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.236 G 0.236 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 94 llr = 815 E-value = 8.9e-043 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 24652254556444298:633 pos.-specific C 552265253434248:1a156 probability G 2::::21::1::21:11:22: matrix T ::2331212:1111::1:111 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 ** * Entropy 1.0 ** * (12.5 bits) 0.8 **** 0.6 * * * ** **** * 0.4 ***** ***** ***** * 0.2 ********************* 0.0 --------------------- Multilevel CCAACCACAAAAACCAACACC consensus AATTTA ACCCCCAA GAA sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8829 425 2.78e-08 CGTCGCTCGC CCAACATCACAAACAAACACC CAACTTGACC 6586 413 4.19e-08 GCAACGTACC CCAAACACCAACAGCAACACA GCAGCACACA 263798 473 4.19e-08 GCACCGTCAC ACAACGACAACCTCCAACACC GACAGCC 20903 469 1.32e-07 CACATACTAT CCCTCCACAATAACCAACACA CACTATTCAC 42365 295 2.26e-07 GGCAACAACA AATACCACAAAAAACAACAAT GGACGATCAA 33794 400 3.17e-07 GACGGGACCC CCCCCCCCCCAACACAACACA CAACTCAACC 5263 265 3.75e-07 GCGATAGAAG CCAACTGCCAACAGCAACAAC GTGACGATGA 14707 442 3.75e-07 AACAGCGCCA GCAACATCACCAGCCAACAAC ACTTGTCGTC 261826 461 4.42e-07 CTCTTGATCT CATACCAACACAAACAACAAT GCTCGCTCCC 10156 349 5.19e-07 GACTTTGGAA CCAATGACAACCCCCAACATC CCCAGAACGG 31569 477 8.30e-07 GCACTCTCTT CCAATCCAACAAACAAACGCA ACC 1393 349 8.30e-07 CTACAGCGAC CAAACCAAACCAAGCAGCAAC ACCCTACATA 25898 478 9.66e-07 CATCTGCCAA GCATTCAAACACATCAACACA CG 8522 50 1.12e-06 AAACCAAAAT CCATCACAACAAACAAACGAC CATGGCACCC 4808 357 1.30e-06 TTCACGAGAG CACACACTCAACAACAACACC TTCACGAATC 24304 454 1.30e-06 ACAACAACTC CCAATCAAACCCCACAACCGC CACCTCTTTA 5431 173 2.00e-06 GTCCATATTG AATATAAAAACAAACAACAAC TTGAAGATGT 32555 460 2.30e-06 AATACAAACA ACAATACAACAATACAACAAC ACCACACTAA 1422 420 2.30e-06 AAACGCCGTC GCTCTCTCAAAAACCAACGAC ATCCGCCGAC 4217 344 2.64e-06 GACGGTCGGC ACACCTACCGACGCCAACAGC ACAAGCAAGC 34210 468 3.94e-06 CAACCTCTCA CAATTCAACCAACTCAACCCC CGCATCGAAA 3124 416 3.94e-06 GCCGACTCTC GCCACAACAAACGCCAACGTC CTCCGACCAC 1111 450 4.49e-06 ATTGTTTAAT TCAACCTCCACAACCATCACC TCTCTTCCCA 9684 45 5.11e-06 GGGAACTTTT GCTTTTAAAAAAAACAACACA CTCTCTCTTC 11918 423 5.11e-06 CAAGCTCGCC CCTCCCACACCAACCACCGCA GCCGCCGCCA 36788 433 5.80e-06 CGCATTGCCA CAACACAAACCTAACAACACT CTCGTCGTCG 15138 435 5.80e-06 TGTTGTGTGT CCAACCACAACCTCCCGCACC TCTTCCTGGA 37398 437 6.57e-06 CTTTTACCAA CAAACTTCAAACGACACCGCC CGCGCCGTTG 23522 389 6.57e-06 CGACACCCAC GCCACCGCCAACAACATCAAC AGCAGTGTCG 7586 408 7.44e-06 TACACTCCTT CAATTCAACACCAACACCACA ATAGCATCAA 36753 445 8.40e-06 GTACACCTCT CCATCGATAAACACCAGCTCC AGTAAGGTCG 6699 466 9.48e-06 ACCTTAGATG CCTACCACTGCCATCAACAAT ACTACAATAC 5009 449 1.07e-05 CACACCTCTA GAATACAACAACCCCAACGTC AATACAGCAC 33513 430 1.07e-05 CCGCACTGTT TCACCCACTCAAATCAACACT AATCTCACCC 262009 72 1.07e-05 GTGAAGACGA ACATCATCTCAAAACAACGAT CAAACAGCGA 25917 421 1.20e-05 AATCATAAAT CACATCATCCACCCAAACACA AACCAATCCA 21094 434 1.20e-05 ACACACAATC ACACACAATCACACCTACACC TCTTTCTTCT 20798 466 1.20e-05 ACAACACACG GCTTCCACAATCGCCACCACC ACAGCCACAA 6356 478 1.35e-05 CCCCTGCCTA AACAAGCCAACCGCCAACAGC CA 4041 401 1.35e-05 GACCCGCAAG ACGACAAACAACAGCAACGAC GGACGACGAC 7092 16 1.51e-05 TTTTACCGCT CTATCCACTCAAATCAACGGC ATATAGAACG 4214 465 1.51e-05 AATTTAACAT CCAATACCACCGGACAACAAC TCAAAAGCCA 25910 449 1.89e-05 TCGATCACAC ACAACCACACCCCGATACACC ACAATCATAC 1622 472 1.89e-05 CGAAGCAATA CATTCCTCTCTTGACAACACC ACACAGCA 7206 253 2.12e-05 AGGTGCACAA CAAATGTAAACACCCATCACA TACACTGGTT 36441 470 2.36e-05 ATTTATCCTA ACCACCCATACTAACAACTCC ATTCTGCAGC 23064 1 2.36e-05 . ACCATTTACAAATACAACGCC CAAACTCACC 22301 475 2.36e-05 TTCTCGCTCT GCAACGGCAACACCAAACGGC ACACA 9991 365 2.63e-05 CTTCACTTTC CATTTCACAAATCAAAACACT CAAAGGTGAG 4170 244 2.63e-05 TCCACAGAAG CATATCAGTAACGCCAACGCA AAGTATAGGA 19793 475 2.63e-05 GATCATCACC ACCAACTCACCCACCAACTAT CTATC 11958 475 2.63e-05 CCGCAACAAA CTAATACACAACACCAACATC AAACC 9993 473 3.25e-05 TTTACCCACT CCACAGAATCTCCCAAACAAC TATCACA 24220 447 3.25e-05 TTCGCTGTTC ACAACGACCGACAACGACTAC AACGACGAAC 7091 176 4.00e-05 GTCAAACAAC TCATCAAATAAAGCAAACACA ACACTCAACA 2376 107 4.00e-05 GACTGCAGCT GAATTCTAACTCACCAACTGC CAACCATTGC 9992 175 4.43e-05 GCAGCCCTTC CCAACTAACGCCGTCGACACC AGACCAGAAC 7100 428 4.43e-05 CAGCGCTAGT AGTTTCAAAAAAGCCAACGGC CAAATCGGTG 35387 284 4.43e-05 AGTTGGCCCA CGATCAACCGAAGCCAACCAC CTCGTCGCCT 11186 413 4.43e-05 ACCACCGACG AACTCCATAATCCACAACAAA TAGGGCTAAC 269422 391 5.41e-05 ACCGATTCAT CCACCTCCACACCCAATCGGC CAAAAGTAAA 23012 470 5.41e-05 CTCTCATCCT CCACAGTAACAACTAAACAGC GGCAATAGCA 4607 22 5.97e-05 TATGGTAATC CAAACCAAACACAACCTCGTC GTAGGTTAGA 20673 199 5.97e-05 CCTGACACTC GATAACACTCCAATCAACGCT ACGACTCATA 11643 58 5.97e-05 AAATTCAATT CCTACGTCAAATGACAACGTA AAAAATACCG 262102 397 6.58e-05 TGACAGTTGG TCTCTCAACGAACGCAACACC TCCGACGGCT 5867 388 7.96e-05 CTGCAGCGTA CAATAAGAAGTCAACAACACA ATCCAAAGGA 33979 473 8.75e-05 GCTCTTTGAT ACACCATCACATCACACCACA ATCCATC 370 479 9.60e-05 GGAGACCCAC CAACCTCCTCAATCCAACCAT A 35968 266 9.60e-05 AAAGAACGCC CACTAACCAGCAATCAACACA TCACTCACTT 1224 463 9.60e-05 CTCTCCCTTC CATCCTCCAACCTCCAACCAA CCACAGGCAG 2267 343 1.05e-04 AACAGCTGAG AACAACATTCAAACCAGCAGC ACTGCTTGAA 4688 189 1.15e-04 AATGGGTTTG CAAATCACTCAACACAACTGG TGAACGGAGG 10002 410 1.15e-04 CCATATCATC ACAACGGACCAACGCCACAGC AAAGGACTGC 5662 463 1.38e-04 TTCTTTATCA AAACACCCCCATATCAGCAAC AGGAGAACCA 10434 388 1.50e-04 TCAATCAAAT CAGTCAAATCAAAGCAACGGA ACGATACGAG 15226 71 2.30e-04 CAAGGGATTT GACTCCACCAAATGCATCCAC AGGTGTCATC 10832 313 2.30e-04 AGAGAGGTGA AGGATCACCACCAACAACAGT ACATAGTTGC 268117 241 2.50e-04 CTGTTCGCGT GAACCGTTCCCACCCAACTCT CTACTCAATC 4729 314 2.71e-04 TTGAGGGTAT GCATTCCATCTCTCAAACGCA AGGATGGACT 263366 399 2.94e-04 TGCTCATACT CATATCCTCAAATAAAACTCA TTCTATTCTA 262006 473 2.94e-04 ACGAGCCTTC CACCATCGCCAAGCCAACTCC CTACATC 37810 294 3.19e-04 TTTGATATCG CCTTCATCCCTCGACGACGAA AGCATGAAGA 35310 451 3.45e-04 GAACCAACGG CAAACGGCCAACAGACACCAC TTCTCTCGCA 260808 159 3.45e-04 GATCTCGATA CACTCCACAAACCGAGGCAGC CATTGTGTTC 32661 144 3.73e-04 CTTTATCGTG AATCCAAACCTTGACAGCAAC CTTGGCAACG 11559 266 3.73e-04 TTCGTACGAC GCAACCGAATAAGCAATCACC GACACGGAAA 9101 20 4.35e-04 CGGCGTCGTC CACAACGACATCTACATCGAC TGCTTGGTTG 8031 183 5.45e-04 CATTAGTAGC AGAACGACCAACACCTGCAAT CATGTCACCA 8536 6 6.78e-04 ACATC CTAACGTGTAAATACAACTAC GGTACGTAGC 23028 432 6.78e-04 CGTCGACCGG CATCATCAAGCAAAAAACGAA CGATCCCTGC 261327 97 7.28e-04 ATAGCAAGTG CCAACGAAAGAAGCAGATACC TGAAATGTTG 268221 334 1.17e-03 TCTTTCTTCT CCAGCTGCCCATCCAAACTCA CGTGGCGGAG 268247 479 1.25e-03 AATAGAGTGG GCAAAGTAAAAGCACAAAACC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8829 2.8e-08 424_[+1]_55 6586 4.2e-08 412_[+1]_67 263798 4.2e-08 472_[+1]_7 20903 1.3e-07 468_[+1]_11 42365 2.3e-07 294_[+1]_185 33794 3.2e-07 399_[+1]_80 5263 3.7e-07 264_[+1]_215 14707 3.7e-07 441_[+1]_38 261826 4.4e-07 460_[+1]_19 10156 5.2e-07 348_[+1]_131 31569 8.3e-07 476_[+1]_3 1393 8.3e-07 348_[+1]_131 25898 9.7e-07 477_[+1]_2 8522 1.1e-06 49_[+1]_430 4808 1.3e-06 356_[+1]_123 24304 1.3e-06 453_[+1]_26 5431 2e-06 172_[+1]_307 32555 2.3e-06 459_[+1]_20 1422 2.3e-06 419_[+1]_60 4217 2.6e-06 343_[+1]_136 34210 3.9e-06 467_[+1]_12 3124 3.9e-06 415_[+1]_64 1111 4.5e-06 449_[+1]_30 9684 5.1e-06 44_[+1]_435 11918 5.1e-06 422_[+1]_57 36788 5.8e-06 432_[+1]_47 15138 5.8e-06 434_[+1]_45 37398 6.6e-06 436_[+1]_43 23522 6.6e-06 388_[+1]_91 7586 7.4e-06 407_[+1]_72 36753 8.4e-06 444_[+1]_35 6699 9.5e-06 465_[+1]_14 5009 1.1e-05 448_[+1]_31 33513 1.1e-05 429_[+1]_50 262009 1.1e-05 71_[+1]_408 25917 1.2e-05 420_[+1]_59 21094 1.2e-05 433_[+1]_46 20798 1.2e-05 465_[+1]_14 6356 1.3e-05 477_[+1]_2 4041 1.3e-05 400_[+1]_79 7092 1.5e-05 15_[+1]_464 4214 1.5e-05 464_[+1]_15 25910 1.9e-05 448_[+1]_31 1622 1.9e-05 471_[+1]_8 7206 2.1e-05 252_[+1]_227 36441 2.4e-05 469_[+1]_10 23064 2.4e-05 [+1]_479 22301 2.4e-05 474_[+1]_5 9991 2.6e-05 364_[+1]_115 4170 2.6e-05 243_[+1]_236 19793 2.6e-05 474_[+1]_5 11958 2.6e-05 474_[+1]_5 9993 3.3e-05 472_[+1]_7 24220 3.3e-05 446_[+1]_33 7091 4e-05 175_[+1]_304 2376 4e-05 106_[+1]_373 9992 4.4e-05 174_[+1]_305 7100 4.4e-05 427_[+1]_52 35387 4.4e-05 283_[+1]_196 11186 4.4e-05 412_[+1]_67 269422 5.4e-05 390_[+1]_89 23012 5.4e-05 469_[+1]_10 4607 6e-05 21_[+1]_458 20673 6e-05 198_[+1]_281 11643 6e-05 57_[+1]_422 262102 6.6e-05 396_[+1]_83 5867 8e-05 387_[+1]_92 33979 8.7e-05 472_[+1]_7 370 9.6e-05 478_[+1]_1 35968 9.6e-05 265_[+1]_214 1224 9.6e-05 462_[+1]_17 2267 0.00011 342_[+1]_137 4688 0.00012 188_[+1]_291 10002 0.00012 409_[+1]_70 5662 0.00014 462_[+1]_17 10434 0.00015 387_[+1]_92 15226 0.00023 70_[+1]_409 10832 0.00023 312_[+1]_167 268117 0.00025 240_[+1]_239 4729 0.00027 313_[+1]_166 263366 0.00029 398_[+1]_81 262006 0.00029 472_[+1]_7 37810 0.00032 293_[+1]_186 35310 0.00034 450_[+1]_29 260808 0.00034 158_[+1]_321 32661 0.00037 143_[+1]_336 11559 0.00037 265_[+1]_214 9101 0.00044 19_[+1]_460 8031 0.00054 182_[+1]_297 8536 0.00068 5_[+1]_474 23028 0.00068 431_[+1]_48 261327 0.00073 96_[+1]_383 268221 0.0012 333_[+1]_146 268247 0.0013 478_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=94 8829 ( 425) CCAACATCACAAACAAACACC 1 6586 ( 413) CCAAACACCAACAGCAACACA 1 263798 ( 473) ACAACGACAACCTCCAACACC 1 20903 ( 469) CCCTCCACAATAACCAACACA 1 42365 ( 295) AATACCACAAAAAACAACAAT 1 33794 ( 400) CCCCCCCCCCAACACAACACA 1 5263 ( 265) CCAACTGCCAACAGCAACAAC 1 14707 ( 442) GCAACATCACCAGCCAACAAC 1 261826 ( 461) CATACCAACACAAACAACAAT 1 10156 ( 349) CCAATGACAACCCCCAACATC 1 31569 ( 477) CCAATCCAACAAACAAACGCA 1 1393 ( 349) CAAACCAAACCAAGCAGCAAC 1 25898 ( 478) GCATTCAAACACATCAACACA 1 8522 ( 50) CCATCACAACAAACAAACGAC 1 4808 ( 357) CACACACTCAACAACAACACC 1 24304 ( 454) CCAATCAAACCCCACAACCGC 1 5431 ( 173) AATATAAAAACAAACAACAAC 1 32555 ( 460) ACAATACAACAATACAACAAC 1 1422 ( 420) GCTCTCTCAAAAACCAACGAC 1 4217 ( 344) ACACCTACCGACGCCAACAGC 1 34210 ( 468) CAATTCAACCAACTCAACCCC 1 3124 ( 416) GCCACAACAAACGCCAACGTC 1 1111 ( 450) TCAACCTCCACAACCATCACC 1 9684 ( 45) GCTTTTAAAAAAAACAACACA 1 11918 ( 423) CCTCCCACACCAACCACCGCA 1 36788 ( 433) CAACACAAACCTAACAACACT 1 15138 ( 435) CCAACCACAACCTCCCGCACC 1 37398 ( 437) CAAACTTCAAACGACACCGCC 1 23522 ( 389) GCCACCGCCAACAACATCAAC 1 7586 ( 408) CAATTCAACACCAACACCACA 1 36753 ( 445) CCATCGATAAACACCAGCTCC 1 6699 ( 466) CCTACCACTGCCATCAACAAT 1 5009 ( 449) GAATACAACAACCCCAACGTC 1 33513 ( 430) TCACCCACTCAAATCAACACT 1 262009 ( 72) ACATCATCTCAAAACAACGAT 1 25917 ( 421) CACATCATCCACCCAAACACA 1 21094 ( 434) ACACACAATCACACCTACACC 1 20798 ( 466) GCTTCCACAATCGCCACCACC 1 6356 ( 478) AACAAGCCAACCGCCAACAGC 1 4041 ( 401) ACGACAAACAACAGCAACGAC 1 7092 ( 16) CTATCCACTCAAATCAACGGC 1 4214 ( 465) CCAATACCACCGGACAACAAC 1 25910 ( 449) ACAACCACACCCCGATACACC 1 1622 ( 472) CATTCCTCTCTTGACAACACC 1 7206 ( 253) CAAATGTAAACACCCATCACA 1 36441 ( 470) ACCACCCATACTAACAACTCC 1 23064 ( 1) ACCATTTACAAATACAACGCC 1 22301 ( 475) GCAACGGCAACACCAAACGGC 1 9991 ( 365) CATTTCACAAATCAAAACACT 1 4170 ( 244) CATATCAGTAACGCCAACGCA 1 19793 ( 475) ACCAACTCACCCACCAACTAT 1 11958 ( 475) CTAATACACAACACCAACATC 1 9993 ( 473) CCACAGAATCTCCCAAACAAC 1 24220 ( 447) ACAACGACCGACAACGACTAC 1 7091 ( 176) TCATCAAATAAAGCAAACACA 1 2376 ( 107) GAATTCTAACTCACCAACTGC 1 9992 ( 175) CCAACTAACGCCGTCGACACC 1 7100 ( 428) AGTTTCAAAAAAGCCAACGGC 1 35387 ( 284) CGATCAACCGAAGCCAACCAC 1 11186 ( 413) AACTCCATAATCCACAACAAA 1 269422 ( 391) CCACCTCCACACCCAATCGGC 1 23012 ( 470) CCACAGTAACAACTAAACAGC 1 4607 ( 22) CAAACCAAACACAACCTCGTC 1 20673 ( 199) GATAACACTCCAATCAACGCT 1 11643 ( 58) CCTACGTCAAATGACAACGTA 1 262102 ( 397) TCTCTCAACGAACGCAACACC 1 5867 ( 388) CAATAAGAAGTCAACAACACA 1 33979 ( 473) ACACCATCACATCACACCACA 1 370 ( 479) CAACCTCCTCAATCCAACCAT 1 35968 ( 266) CACTAACCAGCAATCAACACA 1 1224 ( 463) CATCCTCCAACCTCCAACCAA 1 2267 ( 343) AACAACATTCAAACCAGCAGC 1 4688 ( 189) CAAATCACTCAACACAACTGG 1 10002 ( 410) ACAACGGACCAACGCCACAGC 1 5662 ( 463) AAACACCCCCATATCAGCAAC 1 10434 ( 388) CAGTCAAATCAAAGCAACGGA 1 15226 ( 71) GACTCCACCAAATGCATCCAC 1 10832 ( 313) AGGATCACCACCAACAACAGT 1 268117 ( 241) GAACCGTTCCCACCCAACTCT 1 4729 ( 314) GCATTCCATCTCTCAAACGCA 1 263366 ( 399) CATATCCTCAAATAAAACTCA 1 262006 ( 473) CACCATCGCCAAGCCAACTCC 1 37810 ( 294) CCTTCATCCCTCGACGACGAA 1 35310 ( 451) CAAACGGCCAACAGACACCAC 1 260808 ( 159) CACTCCACAAACCGAGGCAGC 1 32661 ( 144) AATCCAAACCTTGACAGCAAC 1 11559 ( 266) GCAACCGAATAAGCAATCACC 1 9101 ( 20) CACAACGACATCTACATCGAC 1 8031 ( 183) AGAACGACCAACACCTGCAAT 1 8536 ( 6) CTAACGTGTAAATACAACTAC 1 23028 ( 432) CATCATCAAGCAAAAAACGAA 1 261327 ( 97) CCAACGAAAGAAGCAGATACC 1 268221 ( 334) CCAGCTGCCCATCCAAACTCA 1 268247 ( 479) GCAAAGTAAAAGCACAAAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 45120 bayes= 8.90388 E= 8.9e-043 -14 120 -47 -261 55 117 -247 -302 110 -38 -289 -29 95 -22 -447 4 -57 126 -1320 -2 -41 105 -38 -102 95 -30 -130 -44 55 109 -289 -180 83 53 -1320 -52 77 85 -115 -460 115 29 -1320 -115 73 89 -347 -144 73 -1 -22 -115 38 85 -101 -129 -41 176 -1320 -1320 170 -247 -215 -302 153 -215 -147 -161 -466 205 -1320 -460 107 -166 5 -115 25 96 -56 -202 -7 134 -447 -91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 94 E= 8.9e-043 0.244681 0.542553 0.170213 0.042553 0.393617 0.531915 0.042553 0.031915 0.574468 0.180851 0.031915 0.212766 0.521277 0.202128 0.010638 0.265957 0.180851 0.563830 0.000000 0.255319 0.202128 0.489362 0.180851 0.127660 0.521277 0.191489 0.095745 0.191489 0.393617 0.500000 0.031915 0.074468 0.478723 0.340426 0.000000 0.180851 0.457447 0.425532 0.106383 0.010638 0.595745 0.287234 0.000000 0.117021 0.446809 0.436170 0.021277 0.095745 0.446809 0.234043 0.202128 0.117021 0.351064 0.425532 0.117021 0.106383 0.202128 0.797872 0.000000 0.000000 0.872340 0.042553 0.053191 0.031915 0.776596 0.053191 0.085106 0.085106 0.010638 0.978723 0.000000 0.010638 0.563830 0.074468 0.244681 0.117021 0.319149 0.457447 0.159574 0.063830 0.255319 0.595745 0.010638 0.138298 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][CA][AT][ATC][CT][CA]A[CA][AC][AC][AC][AC][ACG][CA][CA]AAC[AG][CA][CA] -------------------------------------------------------------------------------- Time 72.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 56 llr = 589 E-value = 2.0e-027 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::11:21:3::1222::1212 pos.-specific C 1:22::1:21:32:::11111 probability G :823612a3191383282136 matrix T 8244386:38164:5825651 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.0 ** * * * (15.2 bits) 0.8 ** ** * ** * ** 0.6 ** ** * ** * ** * 0.4 ** **** *** **** * * 0.2 ******** ************ 0.0 --------------------- Multilevel TGTTGTTGATGTTGTTGTTTG consensus CGT G G CG G GAGA sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37398 24 2.66e-10 GCGTGGCCAT TGTTGTTGATGCTGATGTTTG TACGGTGGGA 7100 213 2.73e-09 ATGTCGACAC TGCTGTTGATGTTGTTGGCGG TGGCGTGGGT 263798 72 4.76e-09 GAAGAAGAGG TGTTGTTGATGTTGTTGGACG ACGACGGGGA 2376 332 8.14e-09 TGTGGTGTGG TGTGGTTGGTTTTGTGGTTTG TTGGTGGTCG 262009 314 1.89e-08 GACCTGACGA TGGTGTTGATGTTGGTATTGG TAAAGGCGTT 268221 210 3.55e-08 TGCCAATTGA TGTTGGCGATGTTGGTGGTTG TTCATATGGT 14707 10 2.95e-07 CTTTCATCC TGTTGTTGATGTGGTGTTGTA TCTTCGCCGA 7586 77 4.32e-07 AGAGGAGTAT CGTTGTCGTTGTTGTTGTCAG CTTCATGGTT 4688 26 4.32e-07 AGCCGATGAG TGGATATGGTGTTGTTGTTTC GTCGTCGTTG 4217 220 5.53e-07 GTGAGGTCTG TTGTGTGGTTGTGGTGTTTTG TTTCGTGGTA 3124 96 5.53e-07 GGTTGGAGGG TTGGTTTGGGGTGGGTGGTTG TGTAGTGGAG 9993 169 6.25e-07 CAGAATTTTG TTCGTTGGTTGTCGGTGCTTG AGAGAAGGCA 35387 110 7.05e-07 GTTGGCCGTT TGCCGTTGGTTCGATTGTTGG CTGTTTGTCG 36753 116 7.95e-07 CTCGTAGGAG TGTGGTTGCTGTTGTCCGTTG GATGGGAGAG 37810 191 8.94e-07 TTGAATCTAA TGCAGTTGTTGATGTTGGCTG CCGCAAAGCT 8522 382 1.01e-06 TGTGAGTGTA TGTTGTGGTGGTTGGTGCACG TCACTTGTCA 1111 100 1.27e-06 GCCACCCTGG TGGGTTTGCTGTAATTTTATG ATTCCTGATA 11958 297 1.98e-06 ATGCCGGAGA TGGCGTAGCTGTGGATGGATG GAGAGGAGGA 1393 163 2.21e-06 TAAAGTTGAC TTTTTTTGAAGTTGAGGTTTG TACACTGTTG 10002 140 2.21e-06 ATCTTGTATC TTTTTTTGTTGTAGTGTTTGA CGGTGTTTCG 19793 166 2.46e-06 GTCTTGGCCA TGATTTCGATGCGGGGGTTGA GTTGGTTGAA 4808 6 2.74e-06 GGCTC TGTGGTGGCCGTCATTGTTGC TGTGTTCTCT 268247 11 2.74e-06 TGTCGGCGGA TGACGTGGATGTGGATGCTTC GGATTGAGTC 15138 79 2.74e-06 GAACTCATTC TGTAGTTGTTTCAGTTGGTGA TCAGTTGCAA 261826 304 3.38e-06 GGTGATGTGA TGGTATTGATGGCAGTGTTTG ATTGTTGTAG 6356 374 3.75e-06 TGTGTTTGCG AGTTGTGGTTGTGGTGGTGTG TACGACGTCA 33513 246 3.75e-06 TGCAAAGGGC TTCCTTTGATGCTGATGCTAG TATGAACTAC 23522 77 3.75e-06 TTGGATGCAG TGCGGGTGGTGGTGTTGAGTG TATCGTCGAG 9991 468 4.16e-06 AGGGCTGTGA CTTGTGTGCTGTCGGTGTTTG TTGCTGCTGT 9101 246 4.16e-06 GATGTGCGGC TGTTGTGGGTTTGATTGGAAG GCGGTCACTG 25898 226 4.61e-06 TTCTGTTAGT TGTTGACGCGGTAGTGGTTGA AGCGTTCCGC 7091 409 6.87e-06 ACGTTCTATA TGCCGTTGATTTGAGTGGATA GAGCGGTAAA 11643 159 8.34e-06 ATCCTACGCT GGTTGTTGGTGTCGGTGCCGC TTTACATCTC 5662 23 1.01e-05 GCGTTGTGGG CTGCGATGGGGCTGTTGTTGG GAGCTGGGAG 263366 73 1.01e-05 GGGTACAGCA TGTCGATGGTTCTGGTTGTGA TTTGATGCAC 10832 219 1.11e-05 AAACACTCCG TGTGGTGGTCGTTGGTTTGTT TGTTGAGACA 262006 237 1.22e-05 AGCAGTATCG TGGTTTGGATGCGAATTTGTG GAGGAATTAT 261327 163 1.33e-05 TGGGCGAGGC TGGATTTGGTGTTCATGCTGG CTCGGAAGCT 33794 166 1.46e-05 CGTTGGCGGC TGTTGATGAAGCTGGTGCGAG GAAAAGGAGA 25910 285 1.46e-05 GACTCGCGTT TGTGGTAGCGGCAGTGGTCGG AATGGACGAG 1422 165 1.60e-05 AGGAGCGCCA TGGTGTGGTGGTGGTGCGAGG TGCGTGAATA 8031 418 1.75e-05 GAAGATATCC TTCGTTGGTTGATGTTGTAAA GTGAACCTAG 1622 223 1.91e-05 ACCGATCTTC TTCGTACGACGTCGTTGCTTG TTGTTGCCTT 7092 148 2.09e-05 GACCAGGAAA CGTGGTGGGTGCCAATGTTTT ATTTGTGCCT 8829 250 2.28e-05 GAAGGTGTTG TGTTGACGGTGTAGTAGTTCA ATGATCAAGA 6699 417 2.28e-05 AGCGAAGACC TCGTGTTGCTGCTGGTGTACC TCCTGCCTCC 23012 158 2.28e-05 TGTTGCAGCC TGCGGTCGTCTTGGTTGATCG GCAAGTGGCA 42365 457 2.48e-05 CCAACGACGA TGCCGTTGCTGGAGGCGTAGA CGAGAATGTT 22301 52 2.70e-05 TAAACTGTTG TGACGTTGATGTTGATATATT TTGATCGGTA 7206 51 3.48e-05 CTGCGTTCAG TGCTTTTGGTGCAGCTCTCTG CCAGTTTGAT 8536 309 4.10e-05 CCGCCGTCAT TGCGATCGGTGTCGTTGATAC AAGGCACCTT 35310 17 4.10e-05 AAACCGTGTT TGAGTATGATGCAAGTGATGA ATGAGGATAG 1224 194 4.10e-05 CGGAACTGGG CGTTTTTGTCGGCGGTTTTGA TACAACGCTG 2267 80 5.21e-05 GTCAGTATGA CGATGATGCTGAGAGTGTTAG TCATCGCTGA 34210 180 7.12e-05 AGATAGTTGG TGGGTGAGTTGGTGGTGATGA TCCGTGGATT 25917 120 1.11e-04 GCTTTGAGAT GGTGTATGATGATGTGTGATG TATGTCCTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37398 2.7e-10 23_[+2]_456 7100 2.7e-09 212_[+2]_267 263798 4.8e-09 71_[+2]_408 2376 8.1e-09 331_[+2]_148 262009 1.9e-08 313_[+2]_166 268221 3.5e-08 209_[+2]_270 14707 2.9e-07 9_[+2]_470 7586 4.3e-07 76_[+2]_403 4688 4.3e-07 25_[+2]_454 4217 5.5e-07 219_[+2]_260 3124 5.5e-07 95_[+2]_384 9993 6.2e-07 168_[+2]_311 35387 7.1e-07 109_[+2]_370 36753 7.9e-07 115_[+2]_364 37810 8.9e-07 190_[+2]_289 8522 1e-06 381_[+2]_98 1111 1.3e-06 99_[+2]_380 11958 2e-06 296_[+2]_183 1393 2.2e-06 162_[+2]_317 10002 2.2e-06 139_[+2]_340 19793 2.5e-06 165_[+2]_314 4808 2.7e-06 5_[+2]_474 268247 2.7e-06 10_[+2]_469 15138 2.7e-06 78_[+2]_401 261826 3.4e-06 303_[+2]_176 6356 3.8e-06 373_[+2]_106 33513 3.8e-06 245_[+2]_234 23522 3.8e-06 76_[+2]_403 9991 4.2e-06 467_[+2]_12 9101 4.2e-06 245_[+2]_234 25898 4.6e-06 225_[+2]_254 7091 6.9e-06 408_[+2]_71 11643 8.3e-06 158_[+2]_321 5662 1e-05 22_[+2]_457 263366 1e-05 72_[+2]_407 10832 1.1e-05 218_[+2]_261 262006 1.2e-05 236_[+2]_243 261327 1.3e-05 162_[+2]_317 33794 1.5e-05 165_[+2]_314 25910 1.5e-05 284_[+2]_195 1422 1.6e-05 164_[+2]_315 8031 1.7e-05 417_[+2]_62 1622 1.9e-05 222_[+2]_257 7092 2.1e-05 147_[+2]_332 8829 2.3e-05 249_[+2]_230 6699 2.3e-05 416_[+2]_63 23012 2.3e-05 157_[+2]_322 42365 2.5e-05 456_[+2]_23 22301 2.7e-05 51_[+2]_428 7206 3.5e-05 50_[+2]_429 8536 4.1e-05 308_[+2]_171 35310 4.1e-05 16_[+2]_463 1224 4.1e-05 193_[+2]_286 2267 5.2e-05 79_[+2]_400 34210 7.1e-05 179_[+2]_300 25917 0.00011 119_[+2]_360 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=56 37398 ( 24) TGTTGTTGATGCTGATGTTTG 1 7100 ( 213) TGCTGTTGATGTTGTTGGCGG 1 263798 ( 72) TGTTGTTGATGTTGTTGGACG 1 2376 ( 332) TGTGGTTGGTTTTGTGGTTTG 1 262009 ( 314) TGGTGTTGATGTTGGTATTGG 1 268221 ( 210) TGTTGGCGATGTTGGTGGTTG 1 14707 ( 10) TGTTGTTGATGTGGTGTTGTA 1 7586 ( 77) CGTTGTCGTTGTTGTTGTCAG 1 4688 ( 26) TGGATATGGTGTTGTTGTTTC 1 4217 ( 220) TTGTGTGGTTGTGGTGTTTTG 1 3124 ( 96) TTGGTTTGGGGTGGGTGGTTG 1 9993 ( 169) TTCGTTGGTTGTCGGTGCTTG 1 35387 ( 110) TGCCGTTGGTTCGATTGTTGG 1 36753 ( 116) TGTGGTTGCTGTTGTCCGTTG 1 37810 ( 191) TGCAGTTGTTGATGTTGGCTG 1 8522 ( 382) TGTTGTGGTGGTTGGTGCACG 1 1111 ( 100) TGGGTTTGCTGTAATTTTATG 1 11958 ( 297) TGGCGTAGCTGTGGATGGATG 1 1393 ( 163) TTTTTTTGAAGTTGAGGTTTG 1 10002 ( 140) TTTTTTTGTTGTAGTGTTTGA 1 19793 ( 166) TGATTTCGATGCGGGGGTTGA 1 4808 ( 6) TGTGGTGGCCGTCATTGTTGC 1 268247 ( 11) TGACGTGGATGTGGATGCTTC 1 15138 ( 79) TGTAGTTGTTTCAGTTGGTGA 1 261826 ( 304) TGGTATTGATGGCAGTGTTTG 1 6356 ( 374) AGTTGTGGTTGTGGTGGTGTG 1 33513 ( 246) TTCCTTTGATGCTGATGCTAG 1 23522 ( 77) TGCGGGTGGTGGTGTTGAGTG 1 9991 ( 468) CTTGTGTGCTGTCGGTGTTTG 1 9101 ( 246) TGTTGTGGGTTTGATTGGAAG 1 25898 ( 226) TGTTGACGCGGTAGTGGTTGA 1 7091 ( 409) TGCCGTTGATTTGAGTGGATA 1 11643 ( 159) GGTTGTTGGTGTCGGTGCCGC 1 5662 ( 23) CTGCGATGGGGCTGTTGTTGG 1 263366 ( 73) TGTCGATGGTTCTGGTTGTGA 1 10832 ( 219) TGTGGTGGTCGTTGGTTTGTT 1 262006 ( 237) TGGTTTGGATGCGAATTTGTG 1 261327 ( 163) TGGATTTGGTGTTCATGCTGG 1 33794 ( 166) TGTTGATGAAGCTGGTGCGAG 1 25910 ( 285) TGTGGTAGCGGCAGTGGTCGG 1 1422 ( 165) TGGTGTGGTGGTGGTGCGAGG 1 8031 ( 418) TTCGTTGGTTGATGTTGTAAA 1 1622 ( 223) TTCGTACGACGTCGTTGCTTG 1 7092 ( 148) CGTGGTGGGTGCCAATGTTTT 1 8829 ( 250) TGTTGACGGTGTAGTAGTTCA 1 6699 ( 417) TCGTGTTGCTGCTGGTGTACC 1 23012 ( 158) TGCGGTCGTCTTGGTTGATCG 1 42365 ( 457) TGCCGTTGCTGGAGGCGTAGA 1 22301 ( 52) TGACGTTGATGTTGATATATT 1 7206 ( 51) TGCTTTTGGTGCAGCTCTCTG 1 8536 ( 309) TGCGATCGGTGTCGTTGATAC 1 35310 ( 17) TGAGTATGATGCAAGTGATGA 1 1224 ( 194) CGTTTTTGTCGGCGGTTTTGA 1 2267 ( 80) CGATGATGCTGAGAGTGTTAG 1 34210 ( 180) TGGGTGAGTTGGTGGTGATGA 1 25917 ( 120) GGTGTATGATGATGTGTGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 45120 bayes= 10.8757 E= 2.0e-027 -391 -114 -272 169 -1245 -372 177 -54 -159 -2 -2 78 -191 -55 45 78 -291 -1245 145 31 -59 -1245 -172 153 -233 -72 -14 118 -1245 -1245 208 -1245 26 -40 8 -5 -291 -140 -114 156 -1245 -1245 189 -105 -191 9 -140 118 -74 -55 8 72 -59 -372 177 -1245 -74 -372 52 89 -391 -272 -26 153 -291 -214 167 -69 -159 -72 -2 105 -33 -114 -114 114 -110 -140 45 84 -21 -114 136 -228 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 56 E= 2.0e-027 0.017857 0.107143 0.035714 0.839286 0.000000 0.017857 0.803571 0.178571 0.089286 0.232143 0.232143 0.446429 0.071429 0.160714 0.321429 0.446429 0.035714 0.000000 0.642857 0.321429 0.178571 0.000000 0.071429 0.750000 0.053571 0.142857 0.214286 0.589286 0.000000 0.000000 1.000000 0.000000 0.321429 0.178571 0.250000 0.250000 0.035714 0.089286 0.107143 0.767857 0.000000 0.000000 0.875000 0.125000 0.071429 0.250000 0.089286 0.589286 0.160714 0.160714 0.250000 0.428571 0.178571 0.017857 0.803571 0.000000 0.160714 0.017857 0.339286 0.482143 0.017857 0.035714 0.196429 0.750000 0.035714 0.053571 0.750000 0.160714 0.089286 0.142857 0.232143 0.535714 0.214286 0.107143 0.107143 0.571429 0.125000 0.089286 0.321429 0.464286 0.232143 0.107143 0.607143 0.053571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[TCG][TG][GT]T[TG]G[AGT]TG[TC][TG]G[TG]TG[TG][TA][TG][GA] -------------------------------------------------------------------------------- Time 131.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 45 llr = 493 E-value = 1.3e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 115225134231:613544:6 pos.-specific C 1:::::2:3::4:::112::2 probability G 7827828718739184444a1 matrix T 2121:2::3:131323::3:1 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * Entropy 1.0 * ** * * * * (15.8 bits) 0.8 ** ** ** ** * * * 0.6 ** ** ** ** * * * * 0.4 ***** ** ** *** ***** 0.2 *************** ***** 0.0 --------------------- Multilevel GGAGGAGGAGGCGAGGAAAGA consensus T G AC AG T AGGG sequence G T T T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20798 77 6.30e-09 TGCTAGAATG GGAGGAGACGAGGAGAAAAGA TCCACTAGAT 1224 298 3.13e-08 GTTTGTTGGA GGAGGACGAAGTGAGAGGGGA GGGCGGTTCG 36753 149 4.20e-08 TGGGAGAGGG GGTGGTGAAGGCGTGTGCGGA TGCCAGGACG 25910 309 4.85e-08 TGGTCGGAAT GGACGAGACGGCGAGGAGGGA GCCAACCAAC 5662 295 5.59e-08 GGTCAAGAGT GGTGGTGGCGGTGAGCAAAGC AGAAGGAAGC 11958 322 9.71e-08 TGGATGGAGA GGAGGAGACGGTGTGCGGAGC AGTGTGTCGG 6356 265 1.45e-07 GTGGTTGGTT GGTGGTGGAGTCGAGGAGGGG TGAATCGGAC 36788 82 2.41e-07 TGGGCAGCGC GGGGGGGGGGGGGTGAAGGGG GCACAAATCT 261327 207 3.48e-07 AGAGAGTGTG GGTGAAGGAAGCGAGGAAAGG TCCCGTGTCA 268221 128 3.92e-07 CCTAGGGTTA TTAGGAGGCGGGGTGGAAGGC GCCGTGAGAG 24220 3 3.92e-07 AG GGAGGCGATGGAGTGAAGGGA ACACAAAAAG 37398 52 5.57e-07 TTGTACGGTG GGAGGAGGAGGTGGTGGATGG CTTGGAGATG 25898 90 7.00e-07 GTCCATCGCC GGCGGTGGTGGCGAGTGATGT ATACCCTCAC 9101 352 7.83e-07 TTTATGCACC TCAGGAGGAGGTGAGAGGTGA TGGACGAATT 1393 1 8.75e-07 . GGTTAGGGTGGCGATGAGGGA GGTCTTCATG 4607 174 1.50e-06 ATGTGAGAGG TGGGAGGATGGAGAGGAAGGA GCGGAGGCAG 33979 19 1.50e-06 AGAAGTGAAG GGTGAAGGAGGGAAGAAAGGA GGAAGAAAAA 35968 210 1.67e-06 CAATCACGGC GAAGGACGCGACGAGCACAGA GAGAGGCTAC 10434 25 1.67e-06 TTGCAAGTGT GGTGGAGATGATGTATAAAGA TGATGATGAG 6699 32 1.85e-06 GCTAGTGCTA GGAAGGAGCGGCGGGTGGAGA TCAGGTCGCC 20673 24 1.85e-06 GGAAGTGAGC GTTGGGCGTGATGTGGGAAGA GACGACACAA 15226 285 2.27e-06 GTGGCGAGTA GGTTGAAGTGGTGAGAGCTGA GAGCAATTGA 5263 126 3.72e-06 CCATGGTTGG GTGGGGGGGGACGTGACGTGA TTTATGCGGT 370 86 4.09e-06 AATGTGTGTG AGAAATGACGGCGAGAGGAGA GGTCATGCTG 23522 54 4.09e-06 TTTCGTCTTC GGAGGAGGCGTAGTTGGATGC AGTGCGGGTG 9993 109 4.50e-06 AAGGGCTGCC GGAAGTCGACGGGAGGGAGGC GGTGCGAGGA 10156 267 4.50e-06 GGTAAGAGTA GTGAGTGAAAGCGAGGCGAGA AGACATAGCA 42365 376 4.94e-06 AGCCCACAAT GGAAGCGACGACGATGACGGA TGAGAGTGAC 33794 233 5.43e-06 CCGCAACAGA GGAGGACCAGAGGAGTAAGGG TTGGGAACAT 263366 51 5.43e-06 GGGTGGGCAG GGAGGGAGTGGTGGGTACAGC ATGTCGATGG 4217 272 5.95e-06 CGTGGGCGTG AGAGGTGGAGGGGCTGACGGA GACAACGTGA 24304 90 5.95e-06 TAATTTACAA GGAGGAGGAGGCTCAAAATGA GAGAGGAGAG 22301 100 7.81e-06 TGATGGCAGA TGGGATGGTGATGTGTCGAGA TGACACGAGA 9991 445 8.53e-06 ACTGACATGG AGGAGAGGCGACGAGGGCTGT GACTTGTGTG 4214 31 1.11e-05 TCAAAAAAGG CTGGGAGGAAGGGTGTCAAGA CTAAGAAGAA 268247 173 1.11e-05 CACAACTTGA GGAGGAGGACGTGTACCGTGA CATCGTCAGT 2376 238 1.11e-05 TTGCTCAATG CTAGGTGGCGGCGATGACAGT AAGGATGGGT 37810 85 1.31e-05 GAGGATGGAC CGGAGAGATGAGGAGTGAAGT GTATCGTGAT 1622 400 2.15e-05 CTCAAATGAA TGAGGGGAGAGCTAGCAATGA CAACTCAACT 10002 87 2.15e-05 GTGCAAAGGC GAGTGTGGTGGGTAGGAGGGT GGTGGCTAGG 4041 78 2.33e-05 CTGCATGCAA GGAGGGGGGATGTAGTAGGGC TTGTGGGGTT 9684 253 2.52e-05 TAGGCAAGCT GAGGAGCGAGAAGAGTGATGA TTAAAAGTGC 11186 191 2.94e-05 CAAAAATTTA TATTGAGGTAGAGAGTGAAGA GGCTCGAGCT 8829 213 4.61e-05 TGATGAGGTT GGTAGACAAAGTGTTACGTGA CGTGAAGAAG 262009 29 4.96e-05 TGTAGATAGT TGATTGGACGAGGAGAGGTGA ATGTATGAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20798 6.3e-09 76_[+3]_403 1224 3.1e-08 297_[+3]_182 36753 4.2e-08 148_[+3]_331 25910 4.8e-08 308_[+3]_171 5662 5.6e-08 294_[+3]_185 11958 9.7e-08 321_[+3]_158 6356 1.4e-07 264_[+3]_215 36788 2.4e-07 81_[+3]_398 261327 3.5e-07 206_[+3]_273 268221 3.9e-07 127_[+3]_352 24220 3.9e-07 2_[+3]_477 37398 5.6e-07 51_[+3]_428 25898 7e-07 89_[+3]_390 9101 7.8e-07 351_[+3]_128 1393 8.8e-07 [+3]_479 4607 1.5e-06 173_[+3]_306 33979 1.5e-06 18_[+3]_461 35968 1.7e-06 209_[+3]_270 10434 1.7e-06 24_[+3]_455 6699 1.8e-06 31_[+3]_448 20673 1.8e-06 23_[+3]_456 15226 2.3e-06 284_[+3]_195 5263 3.7e-06 125_[+3]_354 370 4.1e-06 85_[+3]_394 23522 4.1e-06 53_[+3]_426 9993 4.5e-06 108_[+3]_371 10156 4.5e-06 266_[+3]_213 42365 4.9e-06 375_[+3]_104 33794 5.4e-06 232_[+3]_247 263366 5.4e-06 50_[+3]_429 4217 6e-06 271_[+3]_208 24304 6e-06 89_[+3]_390 22301 7.8e-06 99_[+3]_380 9991 8.5e-06 444_[+3]_35 4214 1.1e-05 30_[+3]_449 268247 1.1e-05 172_[+3]_307 2376 1.1e-05 237_[+3]_242 37810 1.3e-05 84_[+3]_395 1622 2.2e-05 399_[+3]_80 10002 2.2e-05 86_[+3]_393 4041 2.3e-05 77_[+3]_402 9684 2.5e-05 252_[+3]_227 11186 2.9e-05 190_[+3]_289 8829 4.6e-05 212_[+3]_267 262009 5e-05 28_[+3]_451 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=45 20798 ( 77) GGAGGAGACGAGGAGAAAAGA 1 1224 ( 298) GGAGGACGAAGTGAGAGGGGA 1 36753 ( 149) GGTGGTGAAGGCGTGTGCGGA 1 25910 ( 309) GGACGAGACGGCGAGGAGGGA 1 5662 ( 295) GGTGGTGGCGGTGAGCAAAGC 1 11958 ( 322) GGAGGAGACGGTGTGCGGAGC 1 6356 ( 265) GGTGGTGGAGTCGAGGAGGGG 1 36788 ( 82) GGGGGGGGGGGGGTGAAGGGG 1 261327 ( 207) GGTGAAGGAAGCGAGGAAAGG 1 268221 ( 128) TTAGGAGGCGGGGTGGAAGGC 1 24220 ( 3) GGAGGCGATGGAGTGAAGGGA 1 37398 ( 52) GGAGGAGGAGGTGGTGGATGG 1 25898 ( 90) GGCGGTGGTGGCGAGTGATGT 1 9101 ( 352) TCAGGAGGAGGTGAGAGGTGA 1 1393 ( 1) GGTTAGGGTGGCGATGAGGGA 1 4607 ( 174) TGGGAGGATGGAGAGGAAGGA 1 33979 ( 19) GGTGAAGGAGGGAAGAAAGGA 1 35968 ( 210) GAAGGACGCGACGAGCACAGA 1 10434 ( 25) GGTGGAGATGATGTATAAAGA 1 6699 ( 32) GGAAGGAGCGGCGGGTGGAGA 1 20673 ( 24) GTTGGGCGTGATGTGGGAAGA 1 15226 ( 285) GGTTGAAGTGGTGAGAGCTGA 1 5263 ( 126) GTGGGGGGGGACGTGACGTGA 1 370 ( 86) AGAAATGACGGCGAGAGGAGA 1 23522 ( 54) GGAGGAGGCGTAGTTGGATGC 1 9993 ( 109) GGAAGTCGACGGGAGGGAGGC 1 10156 ( 267) GTGAGTGAAAGCGAGGCGAGA 1 42365 ( 376) GGAAGCGACGACGATGACGGA 1 33794 ( 233) GGAGGACCAGAGGAGTAAGGG 1 263366 ( 51) GGAGGGAGTGGTGGGTACAGC 1 4217 ( 272) AGAGGTGGAGGGGCTGACGGA 1 24304 ( 90) GGAGGAGGAGGCTCAAAATGA 1 22301 ( 100) TGGGATGGTGATGTGTCGAGA 1 9991 ( 445) AGGAGAGGCGACGAGGGCTGT 1 4214 ( 31) CTGGGAGGAAGGGTGTCAAGA 1 268247 ( 173) GGAGGAGGACGTGTACCGTGA 1 2376 ( 238) CTAGGTGGCGGCGATGACAGT 1 37810 ( 85) CGGAGAGATGAGGAGTGAAGT 1 1622 ( 400) TGAGGGGAGAGCTAGCAATGA 1 10002 ( 87) GAGTGTGGTGGGTAGGAGGGT 1 4041 ( 78) GGAGGGGGGATGTAGTAGGGC 1 9684 ( 253) GAGGAGCGAGAAGAGTGATGA 1 11186 ( 191) TATTGAGGTAGAGAGTGAAGA 1 8829 ( 213) GGTAGACAAAGTGTTACGTGA 1 262009 ( 29) TGATTGGACGAGGAGAGGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 45120 bayes= 10.3477 E= 1.3e-016 -201 -182 159 -74 -160 -340 168 -96 93 -340 -9 -9 -60 -340 155 -122 -79 -1214 180 -354 80 -240 5 -9 -201 -60 172 -1214 21 -340 150 -1214 40 29 -141 4 -60 -240 172 -1214 -1 -1214 150 -196 -127 59 18 4 -359 -1214 191 -155 116 -240 -182 15 -201 -1214 172 -74 -1 -108 59 4 86 -82 68 -1214 65 -41 76 -1214 40 -1214 59 15 -1214 -1214 208 -1214 121 -60 -109 -122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 45 E= 1.3e-016 0.066667 0.066667 0.711111 0.155556 0.088889 0.022222 0.755556 0.133333 0.511111 0.022222 0.222222 0.244444 0.177778 0.022222 0.688889 0.111111 0.155556 0.000000 0.822222 0.022222 0.466667 0.044444 0.244444 0.244444 0.066667 0.155556 0.777778 0.000000 0.311111 0.022222 0.666667 0.000000 0.355556 0.288889 0.088889 0.266667 0.177778 0.044444 0.777778 0.000000 0.266667 0.000000 0.666667 0.066667 0.111111 0.355556 0.266667 0.266667 0.022222 0.000000 0.888889 0.088889 0.600000 0.044444 0.066667 0.288889 0.066667 0.000000 0.777778 0.155556 0.266667 0.111111 0.355556 0.266667 0.488889 0.133333 0.377778 0.000000 0.422222 0.177778 0.400000 0.000000 0.355556 0.000000 0.355556 0.288889 0.000000 0.000000 1.000000 0.000000 0.622222 0.155556 0.111111 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GG[ATG]GG[AGT]G[GA][ACT]G[GA][CGT]G[AT]G[GAT][AG][AG][AGT]GA -------------------------------------------------------------------------------- Time 188.89 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10002 6.93e-05 86_[+3(2.15e-05)]_32_[+2(2.21e-06)]_\ 340 10156 4.35e-05 76_[+1(1.07e-05)]_169_\ [+3(4.50e-06)]_61_[+1(5.19e-07)]_131 10434 1.56e-03 24_[+3(1.67e-06)]_455 10832 1.04e-02 218_[+2(1.11e-05)]_261 1111 5.69e-05 99_[+2(1.27e-06)]_329_\ [+1(4.49e-06)]_30 11186 2.90e-03 190_[+3(2.94e-05)]_201_\ [+1(4.43e-05)]_67 11559 2.00e-01 500 11643 2.22e-03 57_[+1(5.97e-05)]_80_[+2(8.34e-06)]_\ 321 11918 7.53e-03 185_[+1(8.75e-05)]_216_\ [+1(5.11e-06)]_57 11958 1.39e-07 296_[+2(1.98e-06)]_4_[+3(9.71e-08)]_\ 132_[+1(2.63e-05)]_5 1224 2.42e-06 193_[+2(4.10e-05)]_83_\ [+3(3.13e-08)]_144_[+1(9.60e-05)]_17 1393 4.89e-08 [+3(8.75e-07)]_141_[+2(2.21e-06)]_\ 165_[+1(8.30e-07)]_110_[+1(4.90e-05)] 1422 3.51e-06 167_[+3(4.94e-06)]_175_\ [+1(8.75e-05)]_35_[+1(2.30e-06)]_38_[+1(3.25e-05)]_1 14707 3.69e-06 9_[+2(2.95e-07)]_386_[+1(1.07e-05)]_\ 4_[+1(3.75e-07)]_38 15138 1.47e-04 78_[+2(2.74e-06)]_74_[+2(5.21e-05)]_\ 240_[+1(5.80e-06)]_45 15226 1.52e-03 284_[+3(2.27e-06)]_195 1622 9.56e-05 222_[+2(1.91e-05)]_156_\ [+3(2.15e-05)]_24_[+1(7.24e-05)]_6_[+1(1.89e-05)]_8 19793 9.61e-04 165_[+2(2.46e-06)]_288_\ [+1(2.63e-05)]_5 20673 6.69e-04 23_[+3(1.85e-06)]_154_\ [+1(5.97e-05)]_281 20798 1.23e-06 76_[+3(6.30e-09)]_368_\ [+1(1.20e-05)]_14 20903 1.77e-03 468_[+1(1.32e-07)]_11 21094 6.00e-02 433_[+1(1.20e-05)]_46 22301 6.49e-05 51_[+2(2.70e-05)]_27_[+3(7.81e-06)]_\ 138_[+3(3.98e-05)]_195_[+1(2.36e-05)]_5 2267 7.35e-03 79_[+2(5.21e-05)]_400 23012 7.80e-03 157_[+2(2.28e-05)]_291_\ [+1(5.41e-05)]_10 23028 7.17e-01 500 23064 1.03e-01 [+1(2.36e-05)]_479 23522 2.08e-06 53_[+3(4.09e-06)]_2_[+2(3.75e-06)]_\ 203_[+1(4.00e-05)]_4_[+1(8.75e-05)]_42_[+1(6.57e-06)]_91 2376 1.01e-07 28_[+3(4.61e-05)]_57_[+1(4.00e-05)]_\ 110_[+3(1.11e-05)]_73_[+2(8.14e-09)]_148 24220 1.10e-04 2_[+3(3.92e-07)]_423_[+1(3.25e-05)]_\ 33 24304 1.26e-04 89_[+3(5.95e-06)]_343_\ [+1(1.30e-06)]_26 25898 8.96e-08 89_[+3(7.00e-07)]_115_\ [+2(4.61e-06)]_231_[+1(9.66e-07)]_2 25910 3.36e-07 284_[+2(1.46e-05)]_3_[+3(4.85e-08)]_\ 119_[+1(1.89e-05)]_31 25917 1.28e-03 420_[+1(1.20e-05)]_59 260808 1.42e-01 500 261327 4.02e-05 162_[+2(1.33e-05)]_23_\ [+3(3.48e-07)]_273 261826 6.02e-06 303_[+2(3.38e-06)]_136_\ [+1(4.42e-07)]_19 262006 6.22e-03 236_[+2(1.22e-05)]_243 262009 2.55e-07 9_[+2(1.91e-05)]_41_[+1(1.07e-05)]_\ 15_[+1(5.41e-05)]_143_[+2(1.01e-06)]_21_[+2(1.89e-08)]_166 262102 1.33e-01 396_[+1(6.58e-05)]_83 263366 1.70e-04 50_[+3(5.43e-06)]_1_[+2(1.01e-05)]_\ 63_[+2(8.93e-05)]_323 263798 1.10e-09 71_[+2(4.76e-09)]_238_\ [+1(1.20e-05)]_4_[+1(4.90e-05)]_96_[+1(4.19e-08)]_7 268117 1.14e-01 500 268221 3.17e-07 62_[+3(1.31e-05)]_44_[+3(3.92e-07)]_\ 61_[+2(3.55e-08)]_28_[+3(1.43e-05)]_221 268247 2.96e-04 10_[+2(2.74e-06)]_141_\ [+3(1.11e-05)]_129_[+2(2.70e-05)]_157 269422 1.99e-01 390_[+1(5.41e-05)]_89 3124 8.84e-06 95_[+2(5.53e-07)]_299_\ [+1(3.94e-06)]_39_[+1(3.25e-05)]_4 31569 6.79e-03 476_[+1(8.30e-07)]_3 32555 4.53e-03 459_[+1(2.30e-06)]_20 32661 7.69e-02 500 33513 4.78e-04 245_[+2(3.75e-06)]_163_\ [+1(1.07e-05)]_50 33794 5.94e-07 165_[+2(1.46e-05)]_46_\ [+3(5.43e-06)]_146_[+1(3.17e-07)]_80 33979 9.18e-04 18_[+3(1.50e-06)]_433_\ [+1(8.75e-05)]_7 34210 1.14e-04 186_[+3(3.43e-05)]_260_\ [+1(3.94e-06)]_12 35310 9.15e-03 16_[+2(4.10e-05)]_463 35387 9.49e-05 7_[+2(1.75e-05)]_81_[+2(7.05e-07)]_\ 153_[+1(4.43e-05)]_196 35968 1.68e-03 209_[+3(1.67e-06)]_35_\ [+1(9.60e-05)]_214 36441 2.00e-02 469_[+1(2.36e-05)]_10 36753 9.84e-09 115_[+2(7.95e-07)]_12_\ [+3(4.20e-08)]_275_[+1(8.40e-06)]_35 36788 2.05e-05 81_[+3(2.41e-07)]_330_\ [+1(5.80e-06)]_47 370 2.35e-03 85_[+3(4.09e-06)]_372_\ [+1(9.60e-05)]_1 37398 5.12e-11 23_[+2(2.66e-10)]_7_[+3(5.57e-07)]_\ 39_[+3(2.94e-05)]_14_[+2(2.28e-05)]_45_[+2(1.11e-05)]_10_[+1(4.43e-05)]_\ 172_[+1(6.57e-06)]_43 37810 4.79e-05 84_[+3(1.31e-05)]_85_[+2(8.94e-07)]_\ 289 4041 2.11e-03 77_[+3(2.33e-05)]_302_\ [+1(1.35e-05)]_79 4170 3.48e-02 243_[+1(2.63e-05)]_236 4214 2.35e-03 30_[+3(1.11e-05)]_413_\ [+1(1.51e-05)]_15 4217 2.28e-07 157_[+2(1.98e-06)]_41_\ [+2(5.53e-07)]_31_[+3(5.95e-06)]_51_[+1(2.64e-06)]_136 42365 6.47e-07 294_[+1(2.26e-07)]_60_\ [+3(4.94e-06)]_60_[+2(2.48e-05)]_23 4607 6.69e-04 21_[+1(5.97e-05)]_131_\ [+3(1.50e-06)]_306 4688 8.44e-04 25_[+2(4.32e-07)]_454 4729 1.65e-01 500 4808 6.87e-05 5_[+2(2.74e-06)]_330_[+1(1.30e-06)]_\ 29_[+1(5.97e-05)]_73 5009 8.14e-03 381_[+1(1.51e-05)]_46_\ [+1(1.07e-05)]_31 5263 1.37e-05 125_[+3(3.72e-06)]_118_\ [+1(3.75e-07)]_49_[+1(4.43e-05)]_145 5431 2.40e-02 172_[+1(2.00e-06)]_307 5662 1.60e-06 22_[+2(1.01e-05)]_18_[+3(1.69e-05)]_\ 212_[+3(5.59e-08)]_185 5867 8.91e-02 387_[+1(7.96e-05)]_92 6356 1.95e-07 264_[+3(1.45e-07)]_88_\ [+2(3.75e-06)]_83_[+1(1.35e-05)]_2 6586 8.22e-04 412_[+1(4.19e-08)]_67 6699 7.07e-06 31_[+3(1.85e-06)]_157_\ [+1(7.96e-05)]_62_[+3(7.05e-05)]_103_[+2(2.28e-05)]_28_[+1(9.48e-06)]_14 7091 2.42e-03 175_[+1(4.00e-05)]_212_\ [+2(6.87e-06)]_71 7092 7.52e-04 15_[+1(1.51e-05)]_111_\ [+2(2.09e-05)]_332 7100 4.85e-07 44_[+2(5.64e-05)]_12_[+2(2.59e-07)]_\ 114_[+2(2.73e-09)]_45_[+2(6.87e-06)]_128_[+1(4.43e-05)]_52 7206 7.60e-03 50_[+2(3.48e-05)]_181_\ [+1(2.12e-05)]_227 7586 3.03e-05 76_[+2(4.32e-07)]_310_\ [+1(7.44e-06)]_72 8031 2.65e-02 417_[+2(1.75e-05)]_62 8522 2.35e-05 49_[+1(1.12e-06)]_61_[+1(7.96e-05)]_\ 229_[+2(1.01e-06)]_47_[+1(5.41e-05)]_30 8536 9.01e-02 308_[+2(4.10e-05)]_171 8829 6.72e-07 212_[+3(4.61e-05)]_16_\ [+2(2.28e-05)]_119_[+1(9.60e-05)]_14_[+1(2.78e-08)]_55 9101 2.00e-05 188_[+2(1.33e-05)]_36_\ [+2(4.16e-06)]_85_[+3(7.83e-07)]_128 9684 3.66e-04 44_[+1(5.11e-06)]_187_\ [+3(2.52e-05)]_227 9991 1.50e-05 364_[+1(2.63e-05)]_59_\ [+3(8.53e-06)]_2_[+2(4.16e-06)]_12 9992 2.09e-01 174_[+1(4.43e-05)]_305 9993 1.89e-06 75_[+2(2.70e-05)]_12_[+3(4.50e-06)]_\ 39_[+2(6.25e-07)]_283_[+1(3.25e-05)]_7 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************