******************************************************************************** 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/220/220.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11949 1.0000 500 13578 1.0000 500 15472 1.0000 500 17145 1.0000 500 17657 1.0000 500 20658 1.0000 500 20985 1.0000 500 21082 1.0000 500 21173 1.0000 500 21222 1.0000 500 21375 1.0000 500 22203 1.0000 500 22204 1.0000 500 22212 1.0000 500 22334 1.0000 500 22404 1.0000 500 22448 1.0000 500 22467 1.0000 500 22582 1.0000 500 22672 1.0000 500 22901 1.0000 500 23187 1.0000 500 23202 1.0000 500 23245 1.0000 500 23650 1.0000 500 23862 1.0000 500 23900 1.0000 500 24016 1.0000 500 24369 1.0000 500 24590 1.0000 500 24712 1.0000 500 24849 1.0000 500 25129 1.0000 500 25183 1.0000 500 25484 1.0000 500 262275 1.0000 500 262326 1.0000 500 262722 1.0000 500 264345 1.0000 500 268130 1.0000 500 268252 1.0000 500 268331 1.0000 500 268559 1.0000 500 268598 1.0000 500 268689 1.0000 500 268735 1.0000 500 268766 1.0000 500 269434 1.0000 500 269776 1.0000 500 2772 1.0000 500 29018 1.0000 500 2921 1.0000 500 30833 1.0000 500 31037 1.0000 500 32374 1.0000 500 32807 1.0000 500 33088 1.0000 500 33425 1.0000 500 34006 1.0000 500 34027 1.0000 500 3583 1.0000 500 36434 1.0000 500 36609 1.0000 500 36798 1.0000 500 37748 1.0000 500 37965 1.0000 500 38006 1.0000 500 38143 1.0000 500 39075 1.0000 500 39540 1.0000 500 39845 1.0000 500 39953 1.0000 500 40529 1.0000 500 40871 1.0000 500 40985 1.0000 500 42282 1.0000 500 42594 1.0000 500 42599 1.0000 500 4624 1.0000 500 7265 1.0000 500 7788 1.0000 500 8336 1.0000 500 bd1515 1.0000 500 bd1667 1.0000 500 bd1876 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/220/220.seqs.fa -oc motifs/220 -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= 85 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= 42500 N= 85 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.237 G 0.242 T 0.255 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.237 G 0.242 T 0.255 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 71 llr = 720 E-value = 2.3e-051 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 225:23248119232942524 pos.-specific C 45367265:79:767:36362 probability G 1211:3112:::1::1::::1 matrix T 3113:2:::2::11::41123 bits 2.1 1.9 1.7 1.5 ** * Relative 1.2 ** * Entropy 1.0 * **** ** (14.6 bits) 0.8 * **** ** * 0.6 ** ********** * 0.4 ** ************** 0.2 ***** *************** 0.0 --------------------- Multilevel CCACCACCACCACCCAACACA consensus TACT GAA AA TAC T sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 32374 453 1.76e-10 TCCCCGTCCA CCACCACCACCACCAACCACT CATTTCTGTG bd1876 44 8.03e-09 GCAGCCTCCT CCACCGCCACCAACAAACCCT CACACAACCC 21222 300 1.35e-08 ACCCTCGACA TCACACCCATCACCCATCACA ACTCATCTTC 22203 437 1.60e-08 CAAACACACA TCACCACAGCCAACCAACCCA CCAGACACTC 39845 7 3.64e-08 CCCACG CCACCGCAGCCACACATCAAC GCTCGAGCAG 21173 397 5.82e-08 CGTCCTCCTC CCACCACAACCACACAAACAC ACTGCAACTG 262275 445 6.77e-08 GCAGCGTTGA CGCTACCAACCACCCATCACA AGTCCTCTTC 7265 346 1.22e-07 GACAACAGAG ACACCGCAGCCACCCATCGCA ACCGTCGCAA 2921 271 1.40e-07 GGAAATGTCG CGGCCACCACCATCCATCCCA TCATCCACGA 268331 413 1.85e-07 TTGGATACAT TAATCACCACCACACAAAACG TCATTTTGAT 22448 415 2.13e-07 CCTGTCCCCT TCATCCAAACCACACATCCAT CACAATCGCC 4624 397 2.44e-07 GAATCACTTC TTCCCACAGCCACACAACACC GCCGAGGACG 22212 327 2.44e-07 TGTCGTTTGC CCCTCTCCACCAATCACCACC TTCAAAACGT 21375 473 2.44e-07 CTGCCAACGA CAACCCCCACAACACAACAAA ACGACGG 25129 302 4.14e-07 CTCAGCCACC CAACCAACAACACCAAACCCA CCCAACCACT 23245 266 4.71e-07 GAGTTGAGAC CACTCCAGACCACCCATCCCT TCCACCTTCC 15472 89 5.35e-07 CTAGGCGACA ACAGCAGCACCACCCATCCTT TTCACGTTTC 25484 90 6.06e-07 ATCTCACAGA ACACCGCAACCTCCCAAACCA TTATCAAATA 268766 402 7.76e-07 AGCAGTGCCA CCATCGGCAACACCAACCCCA ACACCAATTA 13578 116 8.76e-07 ACTTACGGCA CATCATCAATCACCCATCACA GGGAGAAGAC 22582 437 9.88e-07 ACACAAAACC ACACCACCACCCCCCAACCTC ACTGCACTAC 23900 472 1.41e-06 AATTCCCCTC TCACCAACAACACAAACAACA ACATCAAC 24016 431 1.58e-06 ACAGACGAAA CAACAGCACCCACCCAACTCT CGACGAACTG 269776 421 1.77e-06 GGGAGGGGGT TCACCACAGCCAATCAACCTC TTCCCGTCTT 25183 458 1.77e-06 CTCTCGTCGA ACACCTCCACCCTCCACCACA CTCCTCGTCA 23862 406 1.77e-06 TTTTGACATG CTACCACAACCATCCATTTCA CCGTGCCGAC 31037 374 2.77e-06 AAACAGACGT CGACAGCCACCAATCACCCAT TTCGTAACAC 30833 446 2.77e-06 ATACTACTCT CCCTCCACACTACCCATCTCT CTGCCAAGCA 268598 184 3.09e-06 AGCATCATCA CCACCGCCACCACCAGCCTTG CGACGACGTC 264345 218 3.09e-06 GTCAACAACA TCGCCATCACCACACGTCACA TCCAGCATCA 24849 201 3.09e-06 CCCAGGCTAC GCGGCATCACCACCCAACACC AAAATTGCAA 20985 470 3.44e-06 GAACATCAAC GGAGCACAGCCACACAAAACA ACCCCTCAGC 268130 301 4.72e-06 CACCACTGCT GCACACACATCACACACAACA ACATCAACAC 33088 473 7.10e-06 CTCTTTGTTA CAGTCGAAACCAAACAACAAT TGAAACA 36609 265 7.84e-06 ACTCTACCGT CGATCTCAGCCATCCATTCCT CCTCGACCCG 36798 222 8.65e-06 TTTCTTTTTT TAACCGCCACCACAGGCCACA GGCAGAACAG 24712 409 8.65e-06 AGATGCCAGA CACCCGAAACCAGCCAGCACA ACGGAAGGAC 17145 456 8.65e-06 GGTCGCTGTA TCACGCGCATCACCCATCATT TTCTATCTCC 42599 62 9.54e-06 GACATTCAAC GCATAGCCACAACTCATCAAA GGGTTTCCAA 2772 480 1.05e-05 AGTACAGTAT CCATCACGAACACAAATCATC 33425 318 1.16e-05 TCCTCCTCGC CACTCGCGACCACTCACTTCT TGCCTCTGTG 22334 478 1.16e-05 TCGGCCAGGC TCCTTCCACCCACCCACCACC GG 8336 397 1.27e-05 GAATGCTTTT GCTCCCGCACCACTAACCTCA ACCTCTCCAT 39953 53 1.27e-05 CTTGGGCTCT CCATCGGCACCGAACAACACT GTAGACTGCA 268252 444 1.40e-05 CAGCCATCCG TCCTCCCAACAACACAAAGCT TCGCTCCCCA 262326 327 1.40e-05 GCCAATGCGA TTTGCACCGCCACACATCCAC TTCTCTCACT 17657 156 1.40e-05 CTCAATCTAC TCACCAACGACACCCACTAGA TTCCTTAACA 40985 449 1.54e-05 TTCCCGCTCG TTGCCGACACAACCAACCAAA CAAGAGAGGC 23650 410 1.54e-05 AGGTAATAAA TCCTATACATCACACAACCTT CACTCCATCC 40871 475 2.02e-05 ACGCATCACT TCACCGCAACAACAAACACGT CCACC 21082 390 2.21e-05 TTCACTCCTC TGTCCACCACCATCCATTTTT TGATGTTGAG bd1667 322 2.64e-05 CTCTGTGTGT CGCTCTCCACCACCACTCTCT TCGCCTGTTT 268735 434 2.64e-05 AACGTCTGCC CATCATCCGTCACCCATCAAG GCTCAACACT 34027 296 3.14e-05 CTACAACACG ATGGCTCCACCAGCAAACACT GTCGGCGGCA 23187 447 3.14e-05 GGGAAAATAG CTCGCTCGGCCACCCAAAAAC AGTCGAGACA 20658 439 4.06e-05 GAAGGAGACG CCACCGGAGCCAATCAAACTG AACTTGCTCC 32807 412 4.42e-05 AATCTCGACG TAGTCGAAATCACCCATCGAT ACGACTTCGT 24369 474 4.80e-05 ATTCATTATC TCTCACTAACCACTCACAACG CCTCAC 7788 294 5.65e-05 CTCACCTGCA ACCCACCAGCCTCCAACAACA GCAAAACGCA 262722 460 5.65e-05 GAGTGATGTT TACCGCCGACCACTCAATCCA TCAACAAACT 269434 311 6.13e-05 ACCGCTGCTG CAGCATCCACAAGCAAACCCA GCAGTGGCAA 34006 329 7.19e-05 CCACCGTGGC CTACCAACGCTACCAACAATA CCAACAGAGG 23202 366 7.78e-05 GAACTTGGAC CGCCCTGGACCACTCAAAAGT TACCGTAATT 22901 437 8.41e-05 CCTCCATATT TCTTCGCAAACACCCGCTATC TACCGGGAAA 22404 438 9.08e-05 CACCAGATCT TATCACACACAACCCATTCAT CTTGGACCAT 42594 400 1.06e-04 AAAATGCATT GGCGCCAAATCAACCATCTCC ATCTCCATTC 39540 64 1.14e-04 GCAACCAGTG ACCCCGCCATCAGCCGTTCTA GACTCGCTAC 39075 445 1.14e-04 TGTGCGCTTC GCCGTTGAACCATCCATCACA TCAATCTCTC 11949 475 1.23e-04 ATTGTTCAGT ATCCAACCAACAAACAAATCA TCAAA 37748 457 1.32e-04 CAACTTGAGC AGAGCAACATCAACAACAACG ACGACGACGA 22467 422 2.04e-04 TGTATCAGAG AGATCTCACTCAACAAACACG CAAGATCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32374 1.8e-10 452_[+1]_27 bd1876 8e-09 43_[+1]_436 21222 1.4e-08 299_[+1]_180 22203 1.6e-08 436_[+1]_43 39845 3.6e-08 6_[+1]_473 21173 5.8e-08 396_[+1]_83 262275 6.8e-08 444_[+1]_35 7265 1.2e-07 345_[+1]_134 2921 1.4e-07 270_[+1]_209 268331 1.9e-07 412_[+1]_67 22448 2.1e-07 414_[+1]_65 4624 2.4e-07 396_[+1]_83 22212 2.4e-07 326_[+1]_153 21375 2.4e-07 472_[+1]_7 25129 4.1e-07 301_[+1]_178 23245 4.7e-07 265_[+1]_214 15472 5.3e-07 88_[+1]_391 25484 6.1e-07 89_[+1]_390 268766 7.8e-07 401_[+1]_78 13578 8.8e-07 115_[+1]_364 22582 9.9e-07 436_[+1]_43 23900 1.4e-06 471_[+1]_8 24016 1.6e-06 430_[+1]_49 269776 1.8e-06 420_[+1]_59 25183 1.8e-06 457_[+1]_22 23862 1.8e-06 405_[+1]_74 31037 2.8e-06 373_[+1]_106 30833 2.8e-06 445_[+1]_34 268598 3.1e-06 183_[+1]_296 264345 3.1e-06 217_[+1]_262 24849 3.1e-06 200_[+1]_279 20985 3.4e-06 469_[+1]_10 268130 4.7e-06 300_[+1]_179 33088 7.1e-06 472_[+1]_7 36609 7.8e-06 264_[+1]_215 36798 8.7e-06 221_[+1]_258 24712 8.7e-06 408_[+1]_71 17145 8.7e-06 455_[+1]_24 42599 9.5e-06 61_[+1]_418 2772 1.1e-05 479_[+1] 33425 1.2e-05 317_[+1]_162 22334 1.2e-05 477_[+1]_2 8336 1.3e-05 396_[+1]_83 39953 1.3e-05 52_[+1]_427 268252 1.4e-05 443_[+1]_36 262326 1.4e-05 326_[+1]_153 17657 1.4e-05 155_[+1]_324 40985 1.5e-05 448_[+1]_31 23650 1.5e-05 409_[+1]_70 40871 2e-05 474_[+1]_5 21082 2.2e-05 389_[+1]_90 bd1667 2.6e-05 321_[+1]_158 268735 2.6e-05 433_[+1]_46 34027 3.1e-05 295_[+1]_184 23187 3.1e-05 446_[+1]_33 20658 4.1e-05 438_[+1]_41 32807 4.4e-05 411_[+1]_68 24369 4.8e-05 473_[+1]_6 7788 5.7e-05 293_[+1]_186 262722 5.7e-05 459_[+1]_20 269434 6.1e-05 310_[+1]_169 34006 7.2e-05 328_[+1]_151 23202 7.8e-05 365_[+1]_114 22901 8.4e-05 436_[+1]_43 22404 9.1e-05 437_[+1]_42 42594 0.00011 399_[+1]_80 39540 0.00011 63_[+1]_416 39075 0.00011 444_[+1]_35 11949 0.00012 474_[+1]_5 37748 0.00013 456_[+1]_23 22467 0.0002 421_[+1]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=71 32374 ( 453) CCACCACCACCACCAACCACT 1 bd1876 ( 44) CCACCGCCACCAACAAACCCT 1 21222 ( 300) TCACACCCATCACCCATCACA 1 22203 ( 437) TCACCACAGCCAACCAACCCA 1 39845 ( 7) CCACCGCAGCCACACATCAAC 1 21173 ( 397) CCACCACAACCACACAAACAC 1 262275 ( 445) CGCTACCAACCACCCATCACA 1 7265 ( 346) ACACCGCAGCCACCCATCGCA 1 2921 ( 271) CGGCCACCACCATCCATCCCA 1 268331 ( 413) TAATCACCACCACACAAAACG 1 22448 ( 415) TCATCCAAACCACACATCCAT 1 4624 ( 397) TTCCCACAGCCACACAACACC 1 22212 ( 327) CCCTCTCCACCAATCACCACC 1 21375 ( 473) CAACCCCCACAACACAACAAA 1 25129 ( 302) CAACCAACAACACCAAACCCA 1 23245 ( 266) CACTCCAGACCACCCATCCCT 1 15472 ( 89) ACAGCAGCACCACCCATCCTT 1 25484 ( 90) ACACCGCAACCTCCCAAACCA 1 268766 ( 402) CCATCGGCAACACCAACCCCA 1 13578 ( 116) CATCATCAATCACCCATCACA 1 22582 ( 437) ACACCACCACCCCCCAACCTC 1 23900 ( 472) TCACCAACAACACAAACAACA 1 24016 ( 431) CAACAGCACCCACCCAACTCT 1 269776 ( 421) TCACCACAGCCAATCAACCTC 1 25183 ( 458) ACACCTCCACCCTCCACCACA 1 23862 ( 406) CTACCACAACCATCCATTTCA 1 31037 ( 374) CGACAGCCACCAATCACCCAT 1 30833 ( 446) CCCTCCACACTACCCATCTCT 1 268598 ( 184) CCACCGCCACCACCAGCCTTG 1 264345 ( 218) TCGCCATCACCACACGTCACA 1 24849 ( 201) GCGGCATCACCACCCAACACC 1 20985 ( 470) GGAGCACAGCCACACAAAACA 1 268130 ( 301) GCACACACATCACACACAACA 1 33088 ( 473) CAGTCGAAACCAAACAACAAT 1 36609 ( 265) CGATCTCAGCCATCCATTCCT 1 36798 ( 222) TAACCGCCACCACAGGCCACA 1 24712 ( 409) CACCCGAAACCAGCCAGCACA 1 17145 ( 456) TCACGCGCATCACCCATCATT 1 42599 ( 62) GCATAGCCACAACTCATCAAA 1 2772 ( 480) CCATCACGAACACAAATCATC 1 33425 ( 318) CACTCGCGACCACTCACTTCT 1 22334 ( 478) TCCTTCCACCCACCCACCACC 1 8336 ( 397) GCTCCCGCACCACTAACCTCA 1 39953 ( 53) CCATCGGCACCGAACAACACT 1 268252 ( 444) TCCTCCCAACAACACAAAGCT 1 262326 ( 327) TTTGCACCGCCACACATCCAC 1 17657 ( 156) TCACCAACGACACCCACTAGA 1 40985 ( 449) TTGCCGACACAACCAACCAAA 1 23650 ( 410) TCCTATACATCACACAACCTT 1 40871 ( 475) TCACCGCAACAACAAACACGT 1 21082 ( 390) TGTCCACCACCATCCATTTTT 1 bd1667 ( 322) CGCTCTCCACCACCACTCTCT 1 268735 ( 434) CATCATCCGTCACCCATCAAG 1 34027 ( 296) ATGGCTCCACCAGCAAACACT 1 23187 ( 447) CTCGCTCGGCCACCCAAAAAC 1 20658 ( 439) CCACCGGAGCCAATCAAACTG 1 32807 ( 412) TAGTCGAAATCACCCATCGAT 1 24369 ( 474) TCTCACTAACCACTCACAACG 1 7788 ( 294) ACCCACCAGCCTCCAACAACA 1 262722 ( 460) TACCGCCGACCACTCAATCCA 1 269434 ( 311) CAGCATCCACAAGCAAACCCA 1 34006 ( 329) CTACCAACGCTACCAACAATA 1 23202 ( 366) CGCCCTGGACCACTCAAAAGT 1 22901 ( 437) TCTTCGCAAACACCCGCTATC 1 22404 ( 438) TATCACACACAACCCATTCAT 1 42594 ( 400) GGCGCCAAATCAACCATCTCC 1 39540 ( 64) ACCCCGCCATCAGCCGTTCTA 1 39075 ( 445) GCCGTTGAACCATCCATCACA 1 11949 ( 475) ATCCAACCAACAAACAAATCA 1 37748 ( 457) AGAGCAACATCAACAACAACG 1 22467 ( 422) AGATCTCACTCAACAAACACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 40800 bayes= 10.0002 E= 2.3e-051 -78 84 -130 35 -33 114 -64 -118 93 18 -110 -118 -1279 132 -93 14 -43 166 -310 -318 22 -7 22 -48 -24 139 -110 -259 51 118 -152 -1279 151 -248 -30 -1279 -143 166 -1279 -72 -143 188 -1279 -318 180 -307 -410 -318 -66 154 -210 -159 1 132 -1279 -86 -15 166 -410 -1279 178 -407 -178 -1279 40 25 -410 47 -24 145 -1279 -101 93 39 -252 -86 -54 136 -252 -59 62 -37 -130 28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 71 E= 2.3e-051 0.154930 0.422535 0.098592 0.323944 0.211268 0.521127 0.154930 0.112676 0.507042 0.267606 0.112676 0.112676 0.000000 0.591549 0.126761 0.281690 0.197183 0.746479 0.028169 0.028169 0.309859 0.225352 0.281690 0.183099 0.225352 0.619718 0.112676 0.042254 0.380282 0.535211 0.084507 0.000000 0.760563 0.042254 0.197183 0.000000 0.098592 0.746479 0.000000 0.154930 0.098592 0.873239 0.000000 0.028169 0.929577 0.028169 0.014085 0.028169 0.169014 0.690141 0.056338 0.084507 0.267606 0.591549 0.000000 0.140845 0.239437 0.746479 0.014085 0.000000 0.915493 0.014085 0.070423 0.000000 0.352113 0.281690 0.014085 0.352113 0.225352 0.647887 0.000000 0.126761 0.507042 0.309859 0.042254 0.140845 0.183099 0.605634 0.042254 0.169014 0.408451 0.183099 0.098592 0.309859 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CA][AC][CT]C[AGC][CA][CA]ACCAC[CA][CA]A[ATC][CA][AC]C[AT] -------------------------------------------------------------------------------- Time 57.80 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 71 llr = 646 E-value = 2.4e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:13:22121312:32:32:: pos.-specific C 1:2::1:::2:21::1:1::2 probability G 475:75383524283184177 matrix T 533722525253514723631 bits 2.1 1.9 1.7 1.5 Relative 1.2 * Entropy 1.0 * ** * * * * (13.1 bits) 0.8 * ** * * ** ** 0.6 * ** ** * ** *** 0.4 ** ****** * **** *** 0.2 ********************* 0.0 --------------------- Multilevel TGGTGGTGTGTGTGTTGGTGG consensus GTTATTG G ATG G AAT sequence G A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 31037 127 8.22e-08 GTGGTTCCAT TGTTGCTGTGTGTTGTGGTGG ATGGAGGCAG 269434 264 9.75e-08 ATGATGATGT TGTTGGTGGTAGTGGTGATGC AGCCGAGGGA 22204 257 1.60e-07 CGCCTGCGGG GGGTGAGGGGGATGGTGTTGG TAGTTGCATG 7788 22 1.89e-07 AGGACGGGGT TGGAGGGTTGTGTGGTGGATG TACAGTTGCG 37748 245 2.59e-07 GCAATAGTGG TGGAGGAGTTAGTGTAGGTGG TGGGAAGAAG 24369 337 3.52e-07 TTGTGTCGTT GTGTGTTGGGTGGGTTTGTTG ACTTTTTGCC 21082 173 4.75e-07 CAGAAGCTGG TTGTGCGGTGTTCGTTGATGG GCGATCATAT 2921 232 8.45e-07 TTGGATGGTG AGGAGTTGTGACGGTTGTTGG AAATGGCGGG 17657 449 9.71e-07 TTGCTTCTCA TGGTGGAGGGGTGGGTGGAGC ATCTGTAACT 34006 101 1.11e-06 GTAGATGGCC AGGTGAGGGGTGTGGGGGTGG CAAAAATGTG 22672 410 1.11e-06 GAGGGTGCGT GGTTGGGGTCGGGGGTTGTTG TTATGTTGGT 13578 368 1.11e-06 ATGTGAATGA TTTTGGGGGCGATGATGATGG GAGTGAGTCA 268598 372 1.28e-06 TGGTGCAGCT GTGTTGTGTGTGTGGGGGGGG TGAGAGGTCC bd1515 199 1.46e-06 GGAGTGATGG GTGATGGGGGAGTGATGGGGG AATTTGTGTG 22404 12 1.67e-06 AACCTAACTC GTCTGTTGGATTTGGTGTTTG CTCTTGGTGA 268559 342 1.90e-06 AGGAGCATCA TGGTGAGGTGTGTGCTGCTGG GACTATCCCT 20658 11 1.90e-06 ATCATGGCAC GGGAGGAGGATTGGATGGAGG GCATGTCTCC 22582 147 3.16e-06 GCGAAGCTGA GTTTGTTGACTGTGATGGATG AAATGGTTCG 29018 304 3.57e-06 GCATGGTGGT GTGTGGGGTTTGAGGAGTGGG GTTGGTGGTG 3583 286 4.55e-06 AAGATATGGA TTGTGATATCTATGTTGTTGG TGCAGCCAAT 38006 84 5.12e-06 GGCCGTGTAC TGTTGAGTGGAAAGTTGATGG GAAGGGCGGG 22334 22 5.12e-06 GTGAGCGTTG TGTTGTTGTGGACGATGATGC ACGTCGATAT 24849 382 7.26e-06 CCTCCTTTTC TTGTGGTGGAAGAGATTGATG TTTCTAAGCT 38143 116 8.13e-06 TGGTTGGCAA GGTTAGTTTGTGTGGTGTATG CGATGCCTCG 36434 179 8.13e-06 GGGCCATTTC TTCATGTGAGGCAGGTGTTGG CTCGTAATTG 264345 364 8.13e-06 GTAAGTGCCT TGATGTTTTGTCGGGTGTATG ACAGTATGAC 39540 358 1.02e-05 CGCAACAACG TGGAGGAGGAGGAGGAGGAGG AGGAGGACGA 268331 209 1.02e-05 TGGTGTATTG TTCTGTTTTATTTGTAGTTGG CTGGTTCCGG bd1876 163 1.13e-05 GAGGATGGAC TTTAGTTTGGTGTGGAGTTTG CGTGCCGAGG 40529 288 1.13e-05 CCCAAGCGAA TGCAGGAGTCATTGTTGAAGC AAGCAATCGC 22467 65 1.26e-05 CGAGCGGGGC TGCTTGTGAGGCTGATGCTGC CACTGCTCGG 23202 230 1.41e-05 ACTGCAGCCA TGTTTTTGTATTGTTTGGAGG TGTGAGAGAG 21375 223 1.41e-05 GATGCGTAGA GGATGATGTGGTAGTTTATGC ACGCCAATCC 8336 277 1.74e-05 TCGTGTTCTA TGTTGTTGTAGTTGTATATTG TACTCAACCT 33088 327 1.74e-05 ACCTTGATGC GTGATGTGTGGTGCTTGATGG CATCTTCGAC 22901 85 1.74e-05 ATCGGTATGG AGGAGGTGATTTTCATGGTGG TGGCCGGTGT 268252 39 1.93e-05 TTATATTTTT GTTTGGTGTGTTTTTTACTGG CTGATTAGAC 25183 211 1.93e-05 GAATGGAAGC GGCAGTGGTGAAATTTGTTGG AGGCAAGCAA 262275 278 2.13e-05 ACGGCCCTGC AGGTTGGAGGTGTGTTGATGT AAAACAGACT 4624 121 2.36e-05 TGCAGAGTGA TGATGGTGATGCGGACGATGG TAAGGCTCAT 32807 45 2.36e-05 ACGGGATGAG TGGTGGGTAGAGTGATGGACG ATTCGCAATT 23245 153 2.36e-05 TCGTCCGCCA TGGTGATGGAACTGATGTTAG GGAGAGTTGA 7265 53 2.61e-05 TTCTTAACGT GGATGGAGGAAGTGTAGGAGC AATGCAGATT 262326 235 2.61e-05 TCCCGTGTGC AGTATTTGTGTCCGTTGTTTG TGTCTCTCTT 23650 258 2.61e-05 ATTCATCCAA GTGTAGTGTCTTTGTAGTGGG AACCAATCGT 42282 94 3.18e-05 GCGAGCTTGT GGGAGGGGGGAGAGACTGGGG GAGACAAGGT 40985 312 3.50e-05 GGTTGGTGGT TGCTGGAGGGAGGGTGTCTGG GAGGGGGGCG 33425 171 3.85e-05 AAATGGAGAG TGCTGGGTTGTGTTGTGTATT TTTCTATGCA 268689 311 3.85e-05 ACAAGGAGGG CGGTGATTACAGAGGTTGTGG CCACCATGGT 25129 404 4.65e-05 CAAAGCCCCT TGATGCGGTGAAAGTTGAGTG CTGAGTACAG 42594 259 5.11e-05 CACACAGCCA GGGTTGTTGTTGCGTTTGTTC GCAGGCTCGC 39075 378 5.11e-05 GCTTGCTCGT GGTAGGTGTCATTGTTAGTTT GAATTTTGTC 269776 130 5.11e-05 TGGAAGATGT GGATGATGACATTTGTGGATG CACCATCGTT 36609 142 8.00e-05 GTCTTTGCTG TGGAGTTGTTTCGTTCTGTGG GCTCGCTCGC 2772 87 8.72e-05 ATCATTGTAA TTGTTCAGTGTTACGTGATGG GCAGAAGCGT 23187 118 8.72e-05 CAAGGACCTC GTATGTTGTCTCAGAGGGTGC GAACGTTTCT 40871 18 9.50e-05 CTTGCCAGTT GGTTGAAGTTACAGATGAGGC TGTACTTTAA 22448 217 9.50e-05 CAGGAGAGGA GGCAGAAGTGAGTTAAGCTGG ATCATCGTAT 24712 105 1.03e-04 GAGACATACT GTGATGGAACTCGGATGATGG ACGTGATACC 23862 280 1.03e-04 TAACTCGTAT GGCTTGTGTTCATGGAGTTGG ATCGGGAAAG 25484 454 1.13e-04 TCAGCTACCT GCCTGGGGGAGGGGGTGAGGG GAGGGAGCGG 22203 100 1.13e-04 CTTTTGGTGT CGGATGTGGCTTTGGCTGTTG CGGATGGTGC 11949 294 1.13e-04 ATTTGCAAAT CGCTGAGTATTTGGATGGAGG CTATGCAAGA 21222 222 1.22e-04 ACAGCTTCCC CGTTGGTGTGTCCGTATATTT TGCAGAGGTG 20985 31 1.22e-04 GATGCAGCAA TTGTTCTGATAGTGATTGTGT ATGAATACTC 32374 182 1.44e-04 GAGAGGGGCT CGTTGAGATGTCCGTTGTTGT CGGGTGATGT 268766 173 1.44e-04 TGTTTACCCA TTTATGTGATACGTTTGTTTG ATACCTTGTT 39953 119 2.68e-04 GTGCTGTACT GGATGTGATGTGATTTAATGG AAGATGTTCA 22212 61 3.10e-04 GTTCGTACAT TTGAGGATGCAGCGATGGGTC CAGTGGTGAG bd1667 103 3.33e-04 TGGTGGCGAA ATGAGGAGGGGTCGTTGTTGA CTAATTGCGT 24016 61 3.84e-04 AAGATCTCAT CGATAGTGAGGGTGGTGAATT CTCTTCACAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31037 8.2e-08 126_[+2]_353 269434 9.7e-08 263_[+2]_216 22204 1.6e-07 256_[+2]_223 7788 1.9e-07 21_[+2]_458 37748 2.6e-07 244_[+2]_235 24369 3.5e-07 336_[+2]_143 21082 4.7e-07 172_[+2]_307 2921 8.4e-07 231_[+2]_248 17657 9.7e-07 448_[+2]_31 34006 1.1e-06 100_[+2]_379 22672 1.1e-06 409_[+2]_70 13578 1.1e-06 367_[+2]_112 268598 1.3e-06 371_[+2]_108 bd1515 1.5e-06 198_[+2]_281 22404 1.7e-06 11_[+2]_468 268559 1.9e-06 341_[+2]_138 20658 1.9e-06 10_[+2]_469 22582 3.2e-06 146_[+2]_333 29018 3.6e-06 303_[+2]_176 3583 4.5e-06 285_[+2]_194 38006 5.1e-06 83_[+2]_396 22334 5.1e-06 21_[+2]_458 24849 7.3e-06 381_[+2]_98 38143 8.1e-06 115_[+2]_364 36434 8.1e-06 178_[+2]_301 264345 8.1e-06 363_[+2]_116 39540 1e-05 357_[+2]_122 268331 1e-05 208_[+2]_271 bd1876 1.1e-05 162_[+2]_317 40529 1.1e-05 287_[+2]_192 22467 1.3e-05 64_[+2]_415 23202 1.4e-05 229_[+2]_250 21375 1.4e-05 222_[+2]_257 8336 1.7e-05 276_[+2]_203 33088 1.7e-05 326_[+2]_153 22901 1.7e-05 84_[+2]_395 268252 1.9e-05 38_[+2]_441 25183 1.9e-05 210_[+2]_269 262275 2.1e-05 277_[+2]_202 4624 2.4e-05 120_[+2]_359 32807 2.4e-05 44_[+2]_435 23245 2.4e-05 152_[+2]_327 7265 2.6e-05 52_[+2]_427 262326 2.6e-05 234_[+2]_245 23650 2.6e-05 257_[+2]_222 42282 3.2e-05 93_[+2]_386 40985 3.5e-05 311_[+2]_168 33425 3.9e-05 170_[+2]_309 268689 3.9e-05 310_[+2]_169 25129 4.7e-05 403_[+2]_76 42594 5.1e-05 258_[+2]_221 39075 5.1e-05 377_[+2]_102 269776 5.1e-05 129_[+2]_350 36609 8e-05 141_[+2]_338 2772 8.7e-05 86_[+2]_393 23187 8.7e-05 117_[+2]_362 40871 9.5e-05 17_[+2]_462 22448 9.5e-05 216_[+2]_263 24712 0.0001 104_[+2]_375 23862 0.0001 279_[+2]_200 25484 0.00011 453_[+2]_26 22203 0.00011 99_[+2]_380 11949 0.00011 293_[+2]_186 21222 0.00012 221_[+2]_258 20985 0.00012 30_[+2]_449 32374 0.00014 181_[+2]_298 268766 0.00014 172_[+2]_307 39953 0.00027 118_[+2]_361 22212 0.00031 60_[+2]_419 bd1667 0.00033 102_[+2]_377 24016 0.00038 60_[+2]_419 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=71 31037 ( 127) TGTTGCTGTGTGTTGTGGTGG 1 269434 ( 264) TGTTGGTGGTAGTGGTGATGC 1 22204 ( 257) GGGTGAGGGGGATGGTGTTGG 1 7788 ( 22) TGGAGGGTTGTGTGGTGGATG 1 37748 ( 245) TGGAGGAGTTAGTGTAGGTGG 1 24369 ( 337) GTGTGTTGGGTGGGTTTGTTG 1 21082 ( 173) TTGTGCGGTGTTCGTTGATGG 1 2921 ( 232) AGGAGTTGTGACGGTTGTTGG 1 17657 ( 449) TGGTGGAGGGGTGGGTGGAGC 1 34006 ( 101) AGGTGAGGGGTGTGGGGGTGG 1 22672 ( 410) GGTTGGGGTCGGGGGTTGTTG 1 13578 ( 368) TTTTGGGGGCGATGATGATGG 1 268598 ( 372) GTGTTGTGTGTGTGGGGGGGG 1 bd1515 ( 199) GTGATGGGGGAGTGATGGGGG 1 22404 ( 12) GTCTGTTGGATTTGGTGTTTG 1 268559 ( 342) TGGTGAGGTGTGTGCTGCTGG 1 20658 ( 11) GGGAGGAGGATTGGATGGAGG 1 22582 ( 147) GTTTGTTGACTGTGATGGATG 1 29018 ( 304) GTGTGGGGTTTGAGGAGTGGG 1 3583 ( 286) TTGTGATATCTATGTTGTTGG 1 38006 ( 84) TGTTGAGTGGAAAGTTGATGG 1 22334 ( 22) TGTTGTTGTGGACGATGATGC 1 24849 ( 382) TTGTGGTGGAAGAGATTGATG 1 38143 ( 116) GGTTAGTTTGTGTGGTGTATG 1 36434 ( 179) TTCATGTGAGGCAGGTGTTGG 1 264345 ( 364) TGATGTTTTGTCGGGTGTATG 1 39540 ( 358) TGGAGGAGGAGGAGGAGGAGG 1 268331 ( 209) TTCTGTTTTATTTGTAGTTGG 1 bd1876 ( 163) TTTAGTTTGGTGTGGAGTTTG 1 40529 ( 288) TGCAGGAGTCATTGTTGAAGC 1 22467 ( 65) TGCTTGTGAGGCTGATGCTGC 1 23202 ( 230) TGTTTTTGTATTGTTTGGAGG 1 21375 ( 223) GGATGATGTGGTAGTTTATGC 1 8336 ( 277) TGTTGTTGTAGTTGTATATTG 1 33088 ( 327) GTGATGTGTGGTGCTTGATGG 1 22901 ( 85) AGGAGGTGATTTTCATGGTGG 1 268252 ( 39) GTTTGGTGTGTTTTTTACTGG 1 25183 ( 211) GGCAGTGGTGAAATTTGTTGG 1 262275 ( 278) AGGTTGGAGGTGTGTTGATGT 1 4624 ( 121) TGATGGTGATGCGGACGATGG 1 32807 ( 45) TGGTGGGTAGAGTGATGGACG 1 23245 ( 153) TGGTGATGGAACTGATGTTAG 1 7265 ( 53) GGATGGAGGAAGTGTAGGAGC 1 262326 ( 235) AGTATTTGTGTCCGTTGTTTG 1 23650 ( 258) GTGTAGTGTCTTTGTAGTGGG 1 42282 ( 94) GGGAGGGGGGAGAGACTGGGG 1 40985 ( 312) TGCTGGAGGGAGGGTGTCTGG 1 33425 ( 171) TGCTGGGTTGTGTTGTGTATT 1 268689 ( 311) CGGTGATTACAGAGGTTGTGG 1 25129 ( 404) TGATGCGGTGAAAGTTGAGTG 1 42594 ( 259) GGGTTGTTGTTGCGTTTGTTC 1 39075 ( 378) GGTAGGTGTCATTGTTAGTTT 1 269776 ( 130) GGATGATGACATTTGTGGATG 1 36609 ( 142) TGGAGTTGTTTCGTTCTGTGG 1 2772 ( 87) TTGTTCAGTGTTACGTGATGG 1 23187 ( 118) GTATGTTGTCTCAGAGGGTGC 1 40871 ( 18) GGTTGAAGTTACAGATGAGGC 1 22448 ( 217) GGCAGAAGTGAGTTAAGCTGG 1 24712 ( 105) GTGATGGAACTCGGATGATGG 1 23862 ( 280) GGCTTGTGTTCATGGAGTTGG 1 25484 ( 454) GCCTGGGGGAGGGGGTGAGGG 1 22203 ( 100) CGGATGTGGCTTTGGCTGTTG 1 11949 ( 294) CGCTGAGTATTTGGATGGAGG 1 21222 ( 222) CGTTGGTGTGTCCGTATATTT 1 20985 ( 31) TTGTTCTGATAGTGATTGTGT 1 32374 ( 182) CGTTGAGATGTCCGTTGTTGT 1 268766 ( 173) TTTATGTGATACGTTTGTTTG 1 39953 ( 119) GGATGTGATGTGATTTAATGG 1 22212 ( 61) TTGAGGATGCAGCGATGGGTC 1 bd1667 ( 103) ATGAGGAGGGGTCGTTGTTGA 1 24016 ( 61) CGATAGTGAGGGTGGTGAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 40800 bayes= 9.28275 E= 2.4e-019 -166 -149 65 82 -1279 -407 145 35 -107 -49 90 -1 22 -1279 -1279 144 -266 -1279 162 -27 -54 -175 114 -27 -66 -1279 29 107 -192 -1279 165 -59 -54 -1279 42 95 -92 -37 107 -59 22 -407 -20 87 -124 -26 80 7 -43 -107 -20 91 -1279 -248 175 -86 1 -407 42 63 -78 -207 -210 152 -266 -1279 168 -48 1 -175 70 7 -24 -1279 -93 135 -424 -407 148 22 -424 -61 160 -137 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 71 E= 2.4e-019 0.084507 0.084507 0.380282 0.450704 0.000000 0.014085 0.661972 0.323944 0.126761 0.169014 0.450704 0.253521 0.309859 0.000000 0.000000 0.690141 0.042254 0.000000 0.746479 0.211268 0.183099 0.070423 0.535211 0.211268 0.169014 0.000000 0.295775 0.535211 0.070423 0.000000 0.760563 0.169014 0.183099 0.000000 0.323944 0.492958 0.140845 0.183099 0.507042 0.169014 0.309859 0.014085 0.211268 0.464789 0.112676 0.197183 0.422535 0.267606 0.197183 0.112676 0.211268 0.478873 0.000000 0.042254 0.816901 0.140845 0.267606 0.014085 0.323944 0.394366 0.154930 0.056338 0.056338 0.732394 0.042254 0.000000 0.774648 0.183099 0.267606 0.070423 0.394366 0.267606 0.225352 0.000000 0.126761 0.647887 0.014085 0.014085 0.676056 0.295775 0.014085 0.154930 0.732394 0.098592 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][GT][GT][TA][GT][GT][TG]G[TG]G[TAG][GT][TG]G[TGA]TG[GAT][TA][GT]G -------------------------------------------------------------------------------- Time 109.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 18 llr = 261 E-value = 3.2e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1::::1:12::21: pos.-specific C 4:1a:1184:1a:49 probability G 49:::9:2:7::7:: matrix T 1:9:a:9:619:151 bits 2.1 * * 1.9 ** * 1.7 ***** ** * 1.5 ****** ** * Relative 1.2 ******* ** * Entropy 1.0 ******* ** * (20.9 bits) 0.8 ************** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CGTCTGTCTGTCGTC consensus G GCA AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- bd1876 284 2.75e-09 ACTGTGTGGC GGTCTGTCTGTCGTC ATCAAACTGA 42599 367 2.75e-09 CAACATCAGC CGTCTGTCTGTCGCC AAAATATGAA 268689 385 2.75e-09 GTGTATCTTC GGTCTGTCTGTCGCC TGATGCTATG 34006 262 1.13e-08 TTTTCCTCCG CGTCTGTCTGTCACC CAAATCCCCC 7265 281 2.12e-08 TCGCGCCCCC CGTCTGTCCGTCACC GCGGGAAGAC 22212 309 3.93e-08 GTTGTCTCGC GGTCTGTCTGTCGTT TGCCCCTCTC 21222 99 5.32e-08 GTCGTCAGGC GGTCTGTCAGTCGTC CACCAAGAAA 36798 184 6.77e-08 TTCTGACGAC GGTCTGTCCATCATC CGTTTGCCAG 24590 403 8.12e-08 AGTGTCCAGA CGTCTGTGCATCGTC CGTGGTTTCT 24369 445 8.41e-08 TCGTGCATGG CGTCTGACTGTCGTC GGATATTCAT 40985 343 1.13e-07 GAGGGGGGCG CGCCTGTCCGTCGCC GAAGAAAAGT 21375 407 1.13e-07 GCGGTGCCAC CGTCTCTCCGTCGTC CGTCACCGCG 2772 365 1.19e-07 ACTCTTTATC TGTCTGTCTGTCTCC GCTGAGAGAG 262326 282 2.28e-07 ACACTGCACA CGTCTGTCCTTCTCC GTCCACCCCC 22901 312 4.57e-07 GTGGTATAAT GGTCTGCCTGTCGCT CCTCCCCAAA 13578 69 6.78e-07 ACTACAATGT GATCTGTGTATCGTC TGACGCCTCA 32374 51 1.15e-06 TGTTGAACTT GGTCTGTGCTCCGTC TAATAACACC 25129 435 2.15e-06 CTGAGTACAG TGTCTGTGTATCAAC TCTCAGATCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1876 2.7e-09 283_[+3]_202 42599 2.7e-09 366_[+3]_119 268689 2.7e-09 384_[+3]_101 34006 1.1e-08 261_[+3]_224 7265 2.1e-08 280_[+3]_205 22212 3.9e-08 308_[+3]_177 21222 5.3e-08 98_[+3]_387 36798 6.8e-08 183_[+3]_302 24590 8.1e-08 402_[+3]_83 24369 8.4e-08 444_[+3]_41 40985 1.1e-07 342_[+3]_143 21375 1.1e-07 406_[+3]_79 2772 1.2e-07 364_[+3]_121 262326 2.3e-07 281_[+3]_204 22901 4.6e-07 311_[+3]_174 13578 6.8e-07 68_[+3]_417 32374 1.2e-06 50_[+3]_435 25129 2.1e-06 434_[+3]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=18 bd1876 ( 284) GGTCTGTCTGTCGTC 1 42599 ( 367) CGTCTGTCTGTCGCC 1 268689 ( 385) GGTCTGTCTGTCGCC 1 34006 ( 262) CGTCTGTCTGTCACC 1 7265 ( 281) CGTCTGTCCGTCACC 1 22212 ( 309) GGTCTGTCTGTCGTT 1 21222 ( 99) GGTCTGTCAGTCGTC 1 36798 ( 184) GGTCTGTCCATCATC 1 24590 ( 403) CGTCTGTGCATCGTC 1 24369 ( 445) CGTCTGACTGTCGTC 1 40985 ( 343) CGCCTGTCCGTCGCC 1 21375 ( 407) CGTCTCTCCGTCGTC 1 2772 ( 365) TGTCTGTCTGTCTCC 1 262326 ( 282) CGTCTGTCCTTCTCC 1 22901 ( 312) GGTCTGCCTGTCGCT 1 13578 ( 69) GATCTGTGTATCGTC 1 32374 ( 51) GGTCTGTGCTCCGTC 1 25129 ( 435) TGTCTGTGTATCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 41310 bayes= 11.298 E= 3.2e-019 -1081 91 88 -120 -226 -1081 196 -1081 -1081 -209 -1081 189 -1081 208 -1081 -1081 -1081 -1081 -1081 197 -1081 -209 196 -1081 -226 -209 -1081 180 -1081 172 -12 -1081 -226 72 -1081 112 -26 -1081 146 -120 -1081 -209 -1081 189 -1081 208 -1081 -1081 -26 -1081 146 -120 -226 91 -1081 97 -1081 191 -1081 -120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 18 E= 3.2e-019 0.000000 0.444444 0.444444 0.111111 0.055556 0.000000 0.944444 0.000000 0.000000 0.055556 0.000000 0.944444 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.055556 0.944444 0.000000 0.055556 0.055556 0.000000 0.888889 0.000000 0.777778 0.222222 0.000000 0.055556 0.388889 0.000000 0.555556 0.222222 0.000000 0.666667 0.111111 0.000000 0.055556 0.000000 0.944444 0.000000 1.000000 0.000000 0.000000 0.222222 0.000000 0.666667 0.111111 0.055556 0.444444 0.000000 0.500000 0.000000 0.888889 0.000000 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG]GTCTGT[CG][TC][GA]TC[GA][TC]C -------------------------------------------------------------------------------- Time 158.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11949 6.01e-03 32_[+3(8.22e-05)]_453 13578 2.20e-08 68_[+3(6.78e-07)]_32_[+1(8.76e-07)]_\ 192_[+2(1.41e-05)]_18_[+2(1.11e-06)]_112 15472 2.26e-03 88_[+1(5.35e-07)]_63_[+1(1.85e-05)]_\ 265_[+1(2.64e-05)]_[+1(5.80e-06)] 17145 4.45e-03 427_[+3(4.22e-05)]_13_\ [+1(8.65e-06)]_24 17657 1.79e-04 155_[+1(1.40e-05)]_39_\ [+1(7.78e-05)]_212_[+2(9.71e-07)]_31 20658 1.17e-03 10_[+2(1.90e-06)]_78_[+2(1.74e-05)]_\ 308_[+1(4.06e-05)]_41 20985 1.34e-03 469_[+1(3.44e-06)]_10 21082 7.34e-06 151_[+2(2.36e-05)]_[+2(4.75e-07)]_\ 196_[+1(2.21e-05)]_90 21173 3.15e-04 396_[+1(5.82e-08)]_83 21222 3.33e-09 98_[+3(5.32e-08)]_154_\ [+1(4.14e-07)]_11_[+1(1.35e-08)]_180 21375 1.34e-08 222_[+2(1.41e-05)]_163_\ [+3(1.13e-07)]_51_[+1(2.44e-07)]_7 22203 1.40e-05 307_[+1(9.08e-05)]_108_\ [+1(1.60e-08)]_43 22204 6.00e-04 155_[+2(1.41e-05)]_80_\ [+2(1.60e-07)]_49_[+2(4.03e-06)]_123_[+2(2.13e-05)]_9 22212 8.12e-08 308_[+3(3.93e-08)]_3_[+1(2.44e-07)]_\ 153 22334 4.68e-04 21_[+2(5.12e-06)]_435_\ [+1(1.16e-05)]_2 22404 1.94e-04 11_[+2(1.67e-06)]_115_\ [+2(8.00e-05)]_111_[+2(6.13e-05)]_137_[+1(9.08e-05)]_42 22448 1.68e-05 86_[+3(6.33e-05)]_115_\ [+2(9.50e-05)]_123_[+2(8.00e-05)]_33_[+1(2.13e-07)]_2_[+1(8.76e-07)]_42 22467 1.83e-02 64_[+2(1.26e-05)]_10_[+2(5.11e-05)]_\ 384 22582 8.14e-05 146_[+2(3.16e-06)]_248_\ [+1(1.40e-05)]_[+1(9.88e-07)]_43 22672 1.00e-02 409_[+2(1.11e-06)]_70 22901 1.11e-05 84_[+2(1.74e-05)]_206_\ [+3(4.57e-07)]_110_[+1(8.41e-05)]_43 23187 1.44e-02 117_[+2(8.72e-05)]_308_\ [+1(3.14e-05)]_33 23202 1.03e-02 229_[+2(1.41e-05)]_45_\ [+2(6.70e-05)]_49_[+1(7.78e-05)]_114 23245 5.92e-05 152_[+2(2.36e-05)]_92_\ [+1(4.71e-07)]_214 23650 2.59e-03 257_[+2(2.61e-05)]_131_\ [+1(1.54e-05)]_70 23862 1.32e-03 405_[+1(1.77e-06)]_74 23900 4.13e-03 471_[+1(1.41e-06)]_8 24016 4.49e-03 188_[+1(2.64e-05)]_221_\ [+1(1.58e-06)]_49 24369 4.37e-08 336_[+2(3.52e-07)]_87_\ [+3(8.41e-08)]_14_[+1(4.80e-05)]_6 24590 8.64e-04 402_[+3(8.12e-08)]_83 24712 9.17e-04 408_[+1(8.65e-06)]_71 24849 1.91e-04 71_[+2(3.85e-05)]_108_\ [+1(3.09e-06)]_160_[+2(7.26e-06)]_56_[+1(2.64e-05)]_21 25129 9.36e-07 301_[+1(4.14e-07)]_81_\ [+2(4.65e-05)]_10_[+3(2.15e-06)]_51 25183 2.88e-04 210_[+2(1.93e-05)]_181_\ [+1(3.43e-05)]_24_[+1(1.77e-06)]_22 25484 5.01e-04 12_[+1(3.43e-05)]_56_[+1(6.06e-07)]_\ 390 262275 2.86e-05 277_[+2(2.13e-05)]_146_\ [+1(6.77e-08)]_35 262326 1.76e-06 234_[+2(2.61e-05)]_26_\ [+3(2.28e-07)]_30_[+1(1.40e-05)]_153 262722 5.37e-02 459_[+1(5.65e-05)]_20 264345 1.62e-04 217_[+1(3.09e-06)]_125_\ [+2(8.13e-06)]_116 268130 1.16e-03 212_[+3(9.61e-05)]_30_\ [+3(5.73e-05)]_4_[+1(3.73e-05)]_3_[+1(4.72e-06)]_179 268252 5.68e-04 38_[+2(1.93e-05)]_384_\ [+1(1.40e-05)]_14_[+1(2.88e-05)]_1 268331 1.25e-05 208_[+2(1.02e-05)]_183_\ [+1(1.85e-07)]_67 268559 6.26e-03 341_[+2(1.90e-06)]_138 268598 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[+2(3.85e-05)]_126_[+1(1.16e-05)]_162 34006 2.89e-08 100_[+2(1.11e-06)]_140_\ [+3(1.13e-08)]_52_[+1(7.19e-05)]_151 34027 7.47e-02 295_[+1(3.14e-05)]_184 3583 3.30e-02 285_[+2(4.55e-06)]_194 36434 7.48e-02 178_[+2(8.13e-06)]_301 36609 5.42e-03 141_[+2(8.00e-05)]_102_\ [+1(7.84e-06)]_99_[+1(2.88e-05)]_37_[+1(5.65e-05)]_37 36798 1.80e-05 183_[+3(6.77e-08)]_23_\ [+1(8.65e-06)]_258 37748 4.00e-04 244_[+2(2.59e-07)]_235 37965 9.77e-01 500 38006 2.92e-02 83_[+2(5.12e-06)]_155_\ [+2(5.60e-05)]_220 38143 3.10e-03 115_[+2(8.13e-06)]_364 39075 6.18e-03 78_[+2(8.72e-05)]_278_\ [+2(5.11e-05)]_102 39540 1.09e-02 357_[+2(1.02e-05)]_122 39845 1.19e-04 6_[+1(3.64e-08)]_280_[+1(9.81e-05)]_\ 29_[+1(4.14e-07)]_47_[+1(6.64e-05)]_54 39953 5.08e-03 52_[+1(1.27e-05)]_427 40529 8.68e-02 287_[+2(1.13e-05)]_192 40871 9.55e-03 17_[+2(9.50e-05)]_436_\ [+1(2.02e-05)]_5 40985 1.33e-06 311_[+2(3.50e-05)]_10_\ [+3(1.13e-07)]_91_[+1(1.54e-05)]_31 42282 1.05e-01 93_[+2(3.18e-05)]_386 42594 9.53e-03 258_[+2(5.11e-05)]_221 42599 6.93e-07 61_[+1(9.54e-06)]_284_\ [+3(2.75e-09)]_119 4624 9.46e-05 120_[+2(2.36e-05)]_255_\ [+1(2.44e-07)]_83 7265 2.66e-09 52_[+2(2.61e-05)]_207_\ [+3(2.12e-08)]_50_[+1(1.22e-07)]_134 7788 5.55e-05 21_[+2(1.89e-07)]_251_\ [+1(5.65e-05)]_186 8336 1.50e-03 276_[+2(1.74e-05)]_99_\ [+1(1.27e-05)]_83 bd1515 6.60e-03 198_[+2(1.46e-06)]_281 bd1667 1.85e-03 321_[+1(2.64e-05)]_158 bd1876 1.45e-11 43_[+1(8.03e-09)]_98_[+2(1.13e-05)]_\ 100_[+3(2.75e-09)]_202 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************