******************************************************************************** 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/303/303.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10786 1.0000 500 10830 1.0000 500 10989 1.0000 500 11055 1.0000 500 11437 1.0000 500 11484 1.0000 500 11510 1.0000 500 11514 1.0000 500 1849 1.0000 500 21388 1.0000 500 2190 1.0000 500 22571 1.0000 500 25916 1.0000 500 262112 1.0000 500 264691 1.0000 500 33437 1.0000 500 4043 1.0000 500 5476 1.0000 500 5748 1.0000 500 5838 1.0000 500 6287 1.0000 500 6344 1.0000 500 6633 1.0000 500 6637 1.0000 500 7790 1.0000 500 8464 1.0000 500 935 1.0000 500 9998 1.0000 500 bd835 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/303/303.seqs.fa -oc motifs/303 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 29 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 14500 N= 29 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.280 C 0.224 G 0.230 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.280 C 0.224 G 0.230 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 29 llr = 266 E-value = 9.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 41221312:36:39:4 pos.-specific C :::::11:2:111:21 probability G 1266427187:96:85 matrix T 57215417::3::::: bits 2.2 1.9 1.7 1.5 * * Relative 1.3 * * * Entropy 1.1 ** * ** (13.2 bits) 0.9 *** * ** 0.6 ***** ********** 0.4 ***** ********** 0.2 ***** ********** 0.0 ---------------- Multilevel TTGGTTGTGGAGGAGG consensus AG AGA ACAT A CA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 6637 285 3.24e-09 GACTAAAATC TTGGTTGTGGTGGAGG TGATTCATGA 6633 275 3.24e-09 GACTAAAATC TTGGTTGTGGTGGAGG TGATTCATGA 4043 136 6.19e-08 TAGGATTGAG TTGTTGGTGGAGGAGG CGTTGGAGGA 264691 362 1.64e-06 ACGAGCAGAG TTGGTATTGGTGGACG GAACATACAG bd835 381 2.67e-06 AACAAAAAGC TGGTGTGTGGCGGAGG AGTGATTCCT 262112 354 3.00e-06 TTGAACATCG TTGGTTTAGGAGCAGG AGCAATAGGG 10989 147 3.37e-06 TGTTACACTC ATGGGAGTGGTTGAGG ATGTTGGTCT 22571 208 3.78e-06 TTTCAGTTCA ATGGTTCTCAAGGAGG AGGAGGGGCT 7790 384 4.24e-06 ATTGTTGTGT ATAAGAGTGGAGAAGA TTCACTCTGT 33437 162 4.24e-06 CCATTGTTCA TGTGTTGTCGAGGACG AGAACTCCAT 5476 298 8.14e-06 AGGGGCTGGA TTGATGGTGGACGACG ATGCATCGAC 6344 274 1.80e-05 TCATTCTTGG AGGGGTGTGGAGGGGC ACTGTTGGTA 11510 19 1.80e-05 GTTGATTTTG AGAGGGGGGGTGGAGA TAATTTGAAT 11055 58 1.98e-05 TCCCGATGGA AAGATTGTCGAGCAGG CTGATTCAGA 21388 261 2.17e-05 TTTTTAGAGC GTGGAAGTGATGGAGA TTGGCACGAG 10786 98 3.12e-05 ATTGCTGGAT ATGAGATTGAAGAACG TTAGAACCTA 935 419 4.05e-05 AAAGAGGTAC TTTGGGTAGAAGAAGA GGTTAAGAAG 9998 211 4.41e-05 TCTCGCCGAA AGTTTGGTGGTGCAGA TCTCTTTGTG 6287 196 5.21e-05 ACCTAAGGAG AGAAGGGAGAAGAAGG CGAGTGTTAG 1849 244 5.21e-05 TCCCTTGAGC TTTTGCGAGAAGAAGG GATCATCTTC 5748 166 5.66e-05 AAAAGTAAGA TTAGATATGATGGAGA GCAAAGCAGT 8464 164 7.20e-05 ACAGATTTTA TTGGTCCTCGAGAAGC AGTCCTTCCA 5838 21 7.20e-05 AGTTGAATTA ATGAGAGACGAGCACA ATACACTTCA 10830 276 7.78e-05 CGATGTTGAT GGAGGTATCGAGGAGA ACCGTTTGAT 11437 176 8.41e-05 CTGGTGATAG TTGCGCGAGGACGAGG GAAGTCATGT 25916 379 9.79e-05 ACCAGCTGAT AACGTAGTGAAGGACA AAGAACCAAA 11514 206 1.52e-04 GTGAATGTTT TATGTTGTGATGAAGT GACATCTGAT 11484 51 1.52e-04 GAGAGAACAG TTGGTGATGGCGACGA TTGGTTTGAG 2190 212 2.29e-04 GGGGTTGCTA ATGGGAAGGAAGGAAA GTTGCATTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6637 3.2e-09 284_[+1]_200 6633 3.2e-09 274_[+1]_210 4043 6.2e-08 135_[+1]_349 264691 1.6e-06 361_[+1]_123 bd835 2.7e-06 380_[+1]_104 262112 3e-06 353_[+1]_131 10989 3.4e-06 146_[+1]_338 22571 3.8e-06 207_[+1]_277 7790 4.2e-06 383_[+1]_101 33437 4.2e-06 161_[+1]_323 5476 8.1e-06 297_[+1]_187 6344 1.8e-05 273_[+1]_211 11510 1.8e-05 18_[+1]_466 11055 2e-05 57_[+1]_427 21388 2.2e-05 260_[+1]_224 10786 3.1e-05 97_[+1]_387 935 4.1e-05 418_[+1]_66 9998 4.4e-05 210_[+1]_274 6287 5.2e-05 195_[+1]_289 1849 5.2e-05 243_[+1]_241 5748 5.7e-05 165_[+1]_319 8464 7.2e-05 163_[+1]_321 5838 7.2e-05 20_[+1]_464 10830 7.8e-05 275_[+1]_209 11437 8.4e-05 175_[+1]_309 25916 9.8e-05 378_[+1]_106 11514 0.00015 205_[+1]_279 11484 0.00015 50_[+1]_434 2190 0.00023 211_[+1]_273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=29 6637 ( 285) TTGGTTGTGGTGGAGG 1 6633 ( 275) TTGGTTGTGGTGGAGG 1 4043 ( 136) TTGTTGGTGGAGGAGG 1 264691 ( 362) TTGGTATTGGTGGACG 1 bd835 ( 381) TGGTGTGTGGCGGAGG 1 262112 ( 354) TTGGTTTAGGAGCAGG 1 10989 ( 147) ATGGGAGTGGTTGAGG 1 22571 ( 208) ATGGTTCTCAAGGAGG 1 7790 ( 384) ATAAGAGTGGAGAAGA 1 33437 ( 162) TGTGTTGTCGAGGACG 1 5476 ( 298) TTGATGGTGGACGACG 1 6344 ( 274) AGGGGTGTGGAGGGGC 1 11510 ( 19) AGAGGGGGGGTGGAGA 1 11055 ( 58) AAGATTGTCGAGCAGG 1 21388 ( 261) GTGGAAGTGATGGAGA 1 10786 ( 98) ATGAGATTGAAGAACG 1 935 ( 419) TTTGGGTAGAAGAAGA 1 9998 ( 211) AGTTTGGTGGTGCAGA 1 6287 ( 196) AGAAGGGAGAAGAAGG 1 1849 ( 244) TTTTGCGAGAAGAAGG 1 5748 ( 166) TTAGATATGATGGAGA 1 8464 ( 164) TTGGTCCTCGAGAAGC 1 5838 ( 21) ATGAGAGACGAGCACA 1 10830 ( 276) GGAGGTATCGAGGAGA 1 11437 ( 176) TTGCGCGAGGACGAGG 1 25916 ( 379) AACGTAGTGAAGGACA 1 11514 ( 206) TATGTTGTGATGAAGT 1 11484 ( 51) TTGGTGATGGCGACGA 1 2190 ( 212) ATGGGAAGGAAGGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14065 bayes= 8.91886 E= 9.6e-004 56 -1150 -174 96 -144 -1150 7 130 -70 -269 143 -62 -44 -269 143 -95 -202 -1150 96 86 -2 -111 7 51 -102 -170 151 -95 -44 -1150 -174 145 -1150 -11 178 -1150 30 -1150 151 -1150 115 -170 -1150 22 -1150 -170 196 -294 -2 -70 135 -1150 173 -269 -274 -1150 -302 -11 172 -1150 44 -170 117 -294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 29 E= 9.6e-004 0.413793 0.000000 0.068966 0.517241 0.103448 0.000000 0.241379 0.655172 0.172414 0.034483 0.620690 0.172414 0.206897 0.034483 0.620690 0.137931 0.068966 0.000000 0.448276 0.482759 0.275862 0.103448 0.241379 0.379310 0.137931 0.068966 0.655172 0.137931 0.206897 0.000000 0.068966 0.724138 0.000000 0.206897 0.793103 0.000000 0.344828 0.000000 0.655172 0.000000 0.620690 0.068966 0.000000 0.310345 0.000000 0.068966 0.896552 0.034483 0.275862 0.137931 0.586207 0.000000 0.931034 0.034483 0.034483 0.000000 0.034483 0.206897 0.758621 0.000000 0.379310 0.068966 0.517241 0.034483 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA][TG]G[GA][TG][TAG]G[TA][GC][GA][AT]G[GA]A[GC][GA] -------------------------------------------------------------------------------- Time 7.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 21 llr = 204 E-value = 2.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 12:::::1:::: pos.-specific C 6:9:1a:75:73 probability G 31::::::2:11 matrix T :61a9:a23a25 bits 2.2 1.9 * ** 1.7 ** ** * 1.5 ** ** * Relative 1.3 ***** * Entropy 1.1 ***** * (14.0 bits) 0.9 ****** ** 0.6 * ********* 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CTCTTCTCCTCT consensus GA T TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 6633 479 8.24e-08 AAACTCTCTT CTCTTCTCCTCC TCAACATCCA 6637 474 1.82e-07 TCGACAAACT CTCTTCTCTTCT TCTCCTCAAC 11510 446 1.24e-06 ATCGATACCG CTCTTCTACTCT CCTCTTTTCA 935 92 1.71e-06 GCACCGACTC GTCTTCTCGTCC ATGTGTATTG 9998 369 3.47e-06 TGGAAGCCGT GTCTTCTCTTCG TATGAGTCTG 6344 373 4.37e-06 ATCCCTCATT CACTTCTCTTCG AGGGGAACAC 11514 415 4.90e-06 TGATCTTCAA CTCTTCTCTTGT TTATGCCCAT 7790 468 6.22e-06 ACAATTTGTG CACTCCTCCTCT ACACGACATC 1849 390 6.22e-06 AGGAGCATCA CGCTTCTACTCT TTCTGCAGCT 2190 66 7.54e-06 ACGCCAGAGT GGCTTCTCCTTT AGTCAGCAGA 10786 73 9.02e-06 GATACGCAAA CTTTTCTCTTCC TTTATTGCTG 264691 447 1.19e-05 TTGAAGAGAG CACTTCTTCTTT TGAAAAAGAC 10989 352 1.79e-05 TTCCTCCTCT AACTTCTTCTCT GAGAGACTTT 262112 480 2.09e-05 GGCCTCTGTC AGCTTCTCCTTC AACGCCACG 11437 415 2.09e-05 GCTTTCACCA GTCTTATCCTCC TACGTGATTT 8464 360 3.40e-05 TCACCGCCAC CTCTTCTTCACC ACCCTCCCAC bd835 472 5.54e-05 TCATCCTCGT CTCTCCTCGTCA TGGCTTGCTT 6287 483 5.54e-05 AAAGAACGTC CTTTTCTACTTT GAAACA 5748 403 6.39e-05 CGACTAGGCC GTCTGCTCGTCG AAAAACGCAA 33437 280 7.71e-05 CACTTCATAC ACCTTCTCTTTT ACTTGGAGCA 4043 200 1.11e-04 ATTGAGATTA GACTTCTTGTGC AACCTTCGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6633 8.2e-08 478_[+2]_10 6637 1.8e-07 473_[+2]_15 11510 1.2e-06 445_[+2]_43 935 1.7e-06 91_[+2]_397 9998 3.5e-06 368_[+2]_120 6344 4.4e-06 372_[+2]_116 11514 4.9e-06 414_[+2]_74 7790 6.2e-06 467_[+2]_21 1849 6.2e-06 389_[+2]_99 2190 7.5e-06 65_[+2]_423 10786 9e-06 72_[+2]_416 264691 1.2e-05 446_[+2]_42 10989 1.8e-05 351_[+2]_137 262112 2.1e-05 479_[+2]_9 11437 2.1e-05 414_[+2]_74 8464 3.4e-05 359_[+2]_129 bd835 5.5e-05 471_[+2]_17 6287 5.5e-05 482_[+2]_6 5748 6.4e-05 402_[+2]_86 33437 7.7e-05 279_[+2]_209 4043 0.00011 199_[+2]_289 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=21 6633 ( 479) CTCTTCTCCTCC 1 6637 ( 474) CTCTTCTCTTCT 1 11510 ( 446) CTCTTCTACTCT 1 935 ( 92) GTCTTCTCGTCC 1 9998 ( 369) GTCTTCTCTTCG 1 6344 ( 373) CACTTCTCTTCG 1 11514 ( 415) CTCTTCTCTTGT 1 7790 ( 468) CACTCCTCCTCT 1 1849 ( 390) CGCTTCTACTCT 1 2190 ( 66) GGCTTCTCCTTT 1 10786 ( 73) CTTTTCTCTTCC 1 264691 ( 447) CACTTCTTCTTT 1 10989 ( 352) AACTTCTTCTCT 1 262112 ( 480) AGCTTCTCCTTC 1 11437 ( 415) GTCTTATCCTCC 1 8464 ( 360) CTCTTCTTCACC 1 bd835 ( 472) CTCTCCTCGTCA 1 6287 ( 483) CTTTTCTACTTT 1 5748 ( 403) GTCTGCTCGTCG 1 33437 ( 280) ACCTTCTCTTTT 1 4043 ( 200) GACTTCTTGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 14181 bayes= 9.70248 E= 2.1e-003 -97 135 31 -1104 -23 -223 -69 110 -1104 202 -1104 -148 -1104 -1104 -1104 191 -1104 -123 -227 169 -255 209 -1104 -1104 -1104 -1104 -1104 191 -97 158 -1104 -48 -1104 123 -27 10 -255 -1104 -1104 184 -1104 158 -127 -16 -255 58 -69 84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 21 E= 2.1e-003 0.142857 0.571429 0.285714 0.000000 0.238095 0.047619 0.142857 0.571429 0.000000 0.904762 0.000000 0.095238 0.000000 0.000000 0.000000 1.000000 0.000000 0.095238 0.047619 0.857143 0.047619 0.952381 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.666667 0.000000 0.190476 0.000000 0.523810 0.190476 0.285714 0.047619 0.000000 0.000000 0.952381 0.000000 0.666667 0.095238 0.238095 0.047619 0.333333 0.142857 0.476190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CG][TA]CTTCTC[CT]T[CT][TC] -------------------------------------------------------------------------------- Time 14.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 13 llr = 188 E-value = 1.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:395:312a32124:5a5:a pos.-specific C 3671:3622:5:312a2:55: probability G :::::71:6::2243:::15: matrix T 54::5::8::27541:3:::: bits 2.2 * 1.9 * * * * 1.7 * * * * 1.5 * * * * * Relative 1.3 * * * * * * Entropy 1.1 *** * * * * ** (20.9 bits) 0.9 ******* * * * ** 0.6 ************ * **** 0.4 ************ ****** 0.2 ********************* 0.0 --------------------- Multilevel TCCATGCTGACTTGACAAACA consensus CTA ACA A A CTG T CG sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8464 74 1.79e-10 TAAACTGGGT TCCATGCTGAATTTACCACCA ACACAACCAA 11514 437 7.53e-09 TTATGCCCAT TCAAAGCTGAATCGCCTAACA TTGTTGCAAC 11510 168 7.53e-09 TTATCCCCAA TCAAAGCTGAATCGCCTAACA TTGTTGCCAC 6633 294 1.67e-08 GTGGAGGTGA TTCATGATGACATTGCTACGA AACGCGCAAC 6637 304 1.88e-08 GTGGAGGTGA TTCATGATGACATTGCCACGA AACGCGCAGC 5838 188 2.40e-08 CAAATAACAA TCAAACCTGAATCGGCCAAGA CCTCACACAA 9998 478 1.25e-07 TCCAACCACA ACCATCCTCACTTCACAAACA AC 2190 476 2.45e-07 CCACCAACTT CCCCTCCTAACTGTACAAACA CAAC 11055 267 2.45e-07 ACGAAAGCGA CTCATGCAGACGTAACAACGA ACAAACGTGT 7790 210 4.72e-07 CTTGCCTGCT CTCAACCTCACTAGTCAACCA CTTCTTTGCC 935 221 5.74e-07 CACGATGAGT TTCAAGGTGATGTAGCAACGA ATCTGATTCT 6344 150 8.72e-07 TCCGTCACCA CCAATGACAACTCTCCAAGGA GCTGGGGACG 33437 98 1.14e-06 GAAGGTGTCC ACCAAGACAATTGGACTAACA ACTAGGGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8464 1.8e-10 73_[+3]_406 11514 7.5e-09 436_[+3]_43 11510 7.5e-09 167_[+3]_312 6633 1.7e-08 293_[+3]_186 6637 1.9e-08 303_[+3]_176 5838 2.4e-08 187_[+3]_292 9998 1.3e-07 477_[+3]_2 2190 2.5e-07 475_[+3]_4 11055 2.5e-07 266_[+3]_213 7790 4.7e-07 209_[+3]_270 935 5.7e-07 220_[+3]_259 6344 8.7e-07 149_[+3]_330 33437 1.1e-06 97_[+3]_382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=13 8464 ( 74) TCCATGCTGAATTTACCACCA 1 11514 ( 437) TCAAAGCTGAATCGCCTAACA 1 11510 ( 168) TCAAAGCTGAATCGCCTAACA 1 6633 ( 294) TTCATGATGACATTGCTACGA 1 6637 ( 304) TTCATGATGACATTGCCACGA 1 5838 ( 188) TCAAACCTGAATCGGCCAAGA 1 9998 ( 478) ACCATCCTCACTTCACAAACA 1 2190 ( 476) CCCCTCCTAACTGTACAAACA 1 11055 ( 267) CTCATGCAGACGTAACAACGA 1 7790 ( 210) CTCAACCTCACTAGTCAACCA 1 935 ( 221) TTCAAGGTGATGTAGCAACGA 1 6344 ( 150) CCAATGACAACTCTCCAAGGA 1 33437 ( 98) ACCAAGACAATTGGACTAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 10.594 E= 1.4e-003 -86 46 -1035 102 -1035 146 -1035 53 14 163 -1035 -1035 172 -154 -1035 -1035 72 -1035 -1035 102 -1035 46 159 -1035 14 146 -158 -1035 -186 -54 -1035 153 -28 -54 142 -1035 184 -1035 -1035 -1035 14 127 -1035 -79 -86 -1035 -58 138 -186 46 -58 80 -86 -154 74 53 46 5 42 -179 -1035 216 -1035 -1035 72 5 -1035 21 184 -1035 -1035 -1035 72 104 -158 -1035 -1035 127 100 -1035 184 -1035 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 1.4e-003 0.153846 0.307692 0.000000 0.538462 0.000000 0.615385 0.000000 0.384615 0.307692 0.692308 0.000000 0.000000 0.923077 0.076923 0.000000 0.000000 0.461538 0.000000 0.000000 0.538462 0.000000 0.307692 0.692308 0.000000 0.307692 0.615385 0.076923 0.000000 0.076923 0.153846 0.000000 0.769231 0.230769 0.153846 0.615385 0.000000 1.000000 0.000000 0.000000 0.000000 0.307692 0.538462 0.000000 0.153846 0.153846 0.000000 0.153846 0.692308 0.076923 0.307692 0.153846 0.461538 0.153846 0.076923 0.384615 0.384615 0.384615 0.230769 0.307692 0.076923 0.000000 1.000000 0.000000 0.000000 0.461538 0.230769 0.000000 0.307692 1.000000 0.000000 0.000000 0.000000 0.461538 0.461538 0.076923 0.000000 0.000000 0.538462 0.461538 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC][CT][CA]A[TA][GC][CA]T[GA]A[CA]T[TC][GT][AGC]C[ATC]A[AC][CG]A -------------------------------------------------------------------------------- Time 21.68 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10786 1.30e-03 72_[+2(9.02e-06)]_13_[+1(3.12e-05)]_\ 387 10830 2.95e-01 275_[+1(7.78e-05)]_209 10989 7.33e-04 146_[+1(3.37e-06)]_189_\ [+2(1.79e-05)]_137 11055 3.37e-05 57_[+1(1.98e-05)]_193_\ [+3(2.45e-07)]_213 11437 6.39e-03 175_[+1(8.41e-05)]_223_\ [+2(2.09e-05)]_74 11484 6.61e-02 500 11510 6.29e-09 18_[+1(1.80e-05)]_133_\ [+3(7.53e-09)]_171_[+3(2.76e-05)]_65_[+2(1.24e-06)]_43 11514 1.52e-07 414_[+2(4.90e-06)]_10_\ [+3(7.53e-09)]_43 1849 7.80e-04 243_[+1(5.21e-05)]_130_\ [+2(6.22e-06)]_99 21388 5.41e-02 260_[+1(2.17e-05)]_224 2190 7.31e-06 65_[+2(7.54e-06)]_398_\ [+3(2.45e-07)]_4 22571 1.92e-02 207_[+1(3.78e-06)]_277 25916 1.11e-01 378_[+1(9.79e-05)]_106 262112 1.61e-04 128_[+1(3.12e-05)]_209_\ [+1(3.00e-06)]_110_[+2(2.09e-05)]_9 264691 1.25e-04 361_[+1(1.64e-06)]_69_\ [+2(1.19e-05)]_42 33437 6.76e-06 97_[+3(1.14e-06)]_43_[+1(4.24e-06)]_\ 102_[+2(7.71e-05)]_209 4043 8.55e-05 135_[+1(6.19e-08)]_349 5476 9.12e-03 297_[+1(8.14e-06)]_187 5748 7.17e-03 165_[+1(5.66e-05)]_26_\ [+1(7.20e-05)]_179_[+2(6.39e-05)]_86 5838 3.72e-05 20_[+1(7.20e-05)]_151_\ [+3(2.40e-08)]_292 6287 1.67e-02 195_[+1(5.21e-05)]_271_\ [+2(5.54e-05)]_6 6344 1.51e-06 149_[+3(8.72e-07)]_103_\ [+1(1.80e-05)]_83_[+2(4.37e-06)]_116 6633 3.32e-13 274_[+1(3.24e-09)]_3_[+3(1.67e-08)]_\ 164_[+2(8.24e-08)]_10 6637 7.86e-13 284_[+1(3.24e-09)]_3_[+3(1.88e-08)]_\ 149_[+2(1.82e-07)]_15 7790 3.24e-07 209_[+3(4.72e-07)]_153_\ [+1(4.24e-06)]_68_[+2(6.22e-06)]_21 8464 1.49e-08 73_[+3(1.79e-10)]_69_[+1(7.20e-05)]_\ 180_[+2(3.40e-05)]_129 935 9.17e-07 91_[+2(1.71e-06)]_117_\ [+3(5.74e-07)]_177_[+1(4.05e-05)]_66 9998 4.74e-07 95_[+2(1.48e-05)]_103_\ [+1(4.41e-05)]_142_[+2(3.47e-06)]_97_[+3(1.25e-07)]_2 bd835 8.06e-04 380_[+1(2.67e-06)]_75_\ [+2(5.54e-05)]_17 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************