******************************************************************************** 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/307/307.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31741 1.0000 500 42824 1.0000 500 46537 1.0000 500 36928 1.0000 500 48790 1.0000 500 43394 1.0000 500 1862 1.0000 500 43764 1.0000 500 33313 1.0000 500 44043 1.0000 500 44049 1.0000 500 44108 1.0000 500 44200 1.0000 500 50523 1.0000 500 44259 1.0000 500 11308 1.0000 500 44889 1.0000 500 7629 1.0000 500 4918 1.0000 500 45472 1.0000 500 12198 1.0000 500 46222 1.0000 500 44201 1.0000 500 50491 1.0000 500 49135 1.0000 500 48859 1.0000 500 36578 1.0000 500 36022 1.0000 500 45061 1.0000 500 49431 1.0000 500 41473 1.0000 500 47279 1.0000 500 43771 1.0000 500 46271 1.0000 500 35603 1.0000 500 48347 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/307/307.seqs.fa -oc motifs/307 -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= 36 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= 18000 N= 36 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.242 G 0.221 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.243 G 0.221 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 19 llr = 212 E-value = 2.3e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1::a:41::834 pos.-specific C 2:7:a:::7::: probability G 1:3:::9:3171 matrix T 6a:::6:a:115 bits 2.2 2.0 * ** ** 1.7 * ** ** 1.5 * ** ** Relative 1.3 * ** ** Entropy 1.1 **** ***** (16.1 bits) 0.9 ********** 0.7 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTCACTGTCAGT consensus C G A G AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48859 348 7.12e-08 TGTTAGGCAA TTCACTGTCAGT GTCACAATCG 44201 69 7.12e-08 CTGTGTGGTC TTCACTGTCAGT CAGCTCATAT 31741 290 2.11e-07 GGATGTCACT TTCACAGTCAGT TCCGCGTGGT 44889 292 1.00e-06 AAAGAGGCTT TTCACTGTCAAT ACCAACCATA 45472 68 1.09e-06 GGATGGCGAC TTCACTGTCAAA ACCGAGTCGG 49431 222 1.47e-06 ATTATTTCGA TTGACTGTGAGA ACAAACCTAC 33313 433 1.56e-06 TCTTCCGTTA TTCACAGTCAAA CCAAAGTATT 44043 362 1.84e-06 TTTCTCGTTG TTGACAGTGAGA GAGCTTGGAA 36578 67 3.84e-06 CTATTCCGTT GTCACTGTCAGT CTTCCTACCT 44108 371 3.84e-06 AAATTTTACG CTGACTGTGAGT GTGTATCGAG 42824 208 4.56e-06 AATGAAATTG ATGACTGTCAGA CATTGTAGAC 46271 426 4.88e-06 CAGGCGCACA CTCACAGTCAGG GAAGATGGCT 36928 439 5.36e-06 ATAGGCACTA CTGACAGTGAGA AGTGGAGGAC 45061 233 8.10e-06 TTATAATTCC TTCACTATCAGT CGTGCATGGG 46537 383 8.10e-06 AACCGAACGA ATCACAGTCAAT TCACGAACAT 11308 6 8.69e-06 ACTCG CTCACAGTCGGT TCTTCTGGCA 43764 272 1.38e-05 AACGAGAAAA TTCACTGTGGGG GATGGGGGAA 50523 188 1.64e-05 AACACTTGGA TTGACTGTGATA TTGTAGTCCG 36022 319 1.80e-05 TCCGCATCCA TTCACAGTCTAA GATCTAGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48859 7.1e-08 347_[+1]_141 44201 7.1e-08 68_[+1]_420 31741 2.1e-07 289_[+1]_199 44889 1e-06 291_[+1]_197 45472 1.1e-06 67_[+1]_421 49431 1.5e-06 221_[+1]_267 33313 1.6e-06 432_[+1]_56 44043 1.8e-06 361_[+1]_127 36578 3.8e-06 66_[+1]_422 44108 3.8e-06 370_[+1]_118 42824 4.6e-06 207_[+1]_281 46271 4.9e-06 425_[+1]_63 36928 5.4e-06 438_[+1]_50 45061 8.1e-06 232_[+1]_256 46537 8.1e-06 382_[+1]_106 11308 8.7e-06 5_[+1]_483 43764 1.4e-05 271_[+1]_217 50523 1.6e-05 187_[+1]_301 36022 1.8e-05 318_[+1]_170 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=19 48859 ( 348) TTCACTGTCAGT 1 44201 ( 69) TTCACTGTCAGT 1 31741 ( 290) TTCACAGTCAGT 1 44889 ( 292) TTCACTGTCAAT 1 45472 ( 68) TTCACTGTCAAA 1 49431 ( 222) TTGACTGTGAGA 1 33313 ( 433) TTCACAGTCAAA 1 44043 ( 362) TTGACAGTGAGA 1 36578 ( 67) GTCACTGTCAGT 1 44108 ( 371) CTGACTGTGAGT 1 42824 ( 208) ATGACTGTCAGA 1 46271 ( 426) CTCACAGTCAGG 1 36928 ( 439) CTGACAGTGAGA 1 45061 ( 233) TTCACTATCAGT 1 46537 ( 383) ATCACAGTCAAT 1 11308 ( 6) CTCACAGTCGGT 1 43764 ( 272) TTCACTGTGGGG 1 50523 ( 188) TTGACTGTGATA 1 36022 ( 319) TTCACAGTCTAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17604 bayes= 10.7523 E= 2.3e-008 -134 -20 -207 122 -1089 -1089 -1089 189 -1089 150 51 -1089 191 -1089 -1089 -1089 -1089 204 -1089 -1089 66 -1089 -1089 110 -234 -1089 210 -1089 -1089 -1089 -1089 189 -1089 150 51 -1089 166 -1089 -107 -236 -2 -1089 163 -236 66 -1089 -107 81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 19 E= 2.3e-008 0.105263 0.210526 0.052632 0.631579 0.000000 0.000000 0.000000 1.000000 0.000000 0.684211 0.315789 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.421053 0.000000 0.000000 0.578947 0.052632 0.000000 0.947368 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.684211 0.315789 0.000000 0.842105 0.000000 0.105263 0.052632 0.263158 0.000000 0.684211 0.052632 0.421053 0.000000 0.105263 0.473684 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]T[CG]AC[TA]GT[CG]A[GA][TA] -------------------------------------------------------------------------------- Time 10.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 35 llr = 303 E-value = 4.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 33:::::2::123:1: pos.-specific C 5211343:24232212 probability G 1:3::6::31::2::: matrix T 14687:7855753888 bits 2.2 2.0 1.7 1.5 Relative 1.3 * Entropy 1.1 *** * *** (12.5 bits) 0.9 ***** * *** 0.7 ********* *** 0.4 ************ *** 0.2 ************ *** 0.0 ---------------- Multilevel CTTTTGTTTTTTATTT consensus AAG CCC GC CTC C sequence C C C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 45472 96 8.18e-08 TCGGCCGCCG CATTTGCTTTTTGTTT TTTTCGATGT 44259 211 4.65e-07 GTTTTTCCGT CTTTTGTTCTTAATTT CTTACACCGG 36022 454 1.08e-06 AAGCAGCCCA CATTCGTTTTTTTTTC AAAACCCGCA 46271 221 1.71e-06 TTGCCACCTG CCTTTGCTGTTAATTT TGATATGGTT 36578 15 2.27e-06 GGGTTGCTTG CCTTCGTTTCCCATTT TCTTTGTTTG 49135 336 2.27e-06 CTTCCAAATG CATTCCTTTTTCATTC CATGGAATAG 11308 52 2.96e-06 CTGGAATCCA GCTTTGCTTTTCTTTT GGTAGCCTGG 43764 75 2.96e-06 ATAATGAAAA CTGTTGTAGTTTGTTT CAGCTCTCTA 31741 206 6.25e-06 TCCGATCTAC CTCTTCTTTTTCGTTT ACAGTTTGAT 42824 106 7.05e-06 AGGACAGACA AATTTCCTCTTCTTTT GACTGTTATA 46537 84 7.90e-06 AATGTGAGTA GAGTCCTTTTTTTTTT AAATCAACGA 44201 457 1.23e-05 ATTTTTTTCA CATTTCTTGCTCATCT CTTTCGCAAG 44889 468 2.05e-05 CGGAATAGCA CTTTTGTTCTTTGCAT TTCGTTCTCA 43394 457 2.05e-05 ACAACATAAC ACTCTGTTTCTCATTC TGCGGTTTCC 49431 111 2.27e-05 GGATTCCATG CTGTTCTTCCATATTT CTACTCGGAA 48859 370 2.27e-05 GTCACAATCG CATTCGTTCCATTTTT CGTGTTCGAT 44108 446 3.03e-05 ATCACAGTCA ATTCTGTTGTTCCCTT GCAGATATAC 48790 386 3.32e-05 ACAAACCCTG ATTTCGTAGTTTTTTC CAAAATGATG 41473 117 3.65e-05 GTGACAACGT CTTTTGCAGCTATTTC TTAGATATAC 47279 12 4.00e-05 GGACCAAATG TATTCGTTGCTTGCTT GCTTACTTGC 45061 20 4.00e-05 TAAGATGACA AAGTTCTTTCCTCCTT ACTGTTTATC 50523 282 4.37e-05 AAAAAGTTGA GTGTCCCTTCCCATTT CCTGTCACAG 35603 278 5.68e-05 CCATTCCGGC GTTTTCCATTTTTCTT CCCTATCTAA 36928 62 5.68e-05 ATTTCTGTTC AACTTGTTTTTTATAT TGTAACGATT 50491 321 6.18e-05 CGGCCTACTA CCTTCCTTTCCCACTC TACTTTCGTA 44043 305 7.92e-05 AAAGTGGCCT CCGATGTTTCTACTTT GCAGGTGATA 4918 149 1.17e-04 TCAAGGACGT CATTCGCACCTTGCTC CAGGTTCCTC 33313 294 1.27e-04 TGGCGCATGC GTGTTCTAGGTTATTT TCCTTTTGAT 44049 62 1.58e-04 TTAAGGACCT CTTTTCTTTGCCTTAT TCAGCTGACC 1862 80 1.82e-04 TAAATGGAGT ACGTTGCTTCCTCTCT TACTCTGGAG 48347 423 1.95e-04 TCCTCCCCTC TTTTTGTTTCTACTGT AAAATCCAAA 43771 109 1.95e-04 ACCGATCTTA CCGTTGCTCCGACTTT CGCCGAAACG 46222 205 2.73e-04 CGTATCTGAT ATAGTGTTGTTTATTT GCATAAGTCA 44200 104 3.74e-04 CTGCACCCAA CAGCTCATTTTCGTTC CCGTGCTCAC 12198 357 4.48e-04 GGGCCGTGAC ATTCCGCTTATTCCTT TTGAAGAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45472 8.2e-08 95_[+2]_389 44259 4.7e-07 210_[+2]_274 36022 1.1e-06 453_[+2]_31 46271 1.7e-06 220_[+2]_264 36578 2.3e-06 14_[+2]_470 49135 2.3e-06 335_[+2]_149 11308 3e-06 51_[+2]_433 43764 3e-06 74_[+2]_410 31741 6.2e-06 205_[+2]_279 42824 7e-06 105_[+2]_379 46537 7.9e-06 83_[+2]_401 44201 1.2e-05 456_[+2]_28 44889 2.1e-05 467_[+2]_17 43394 2.1e-05 456_[+2]_28 49431 2.3e-05 110_[+2]_374 48859 2.3e-05 369_[+2]_115 44108 3e-05 445_[+2]_39 48790 3.3e-05 385_[+2]_99 41473 3.6e-05 116_[+2]_368 47279 4e-05 11_[+2]_473 45061 4e-05 19_[+2]_465 50523 4.4e-05 281_[+2]_203 35603 5.7e-05 277_[+2]_207 36928 5.7e-05 61_[+2]_423 50491 6.2e-05 320_[+2]_164 44043 7.9e-05 304_[+2]_180 4918 0.00012 148_[+2]_336 33313 0.00013 293_[+2]_191 44049 0.00016 61_[+2]_423 1862 0.00018 79_[+2]_405 48347 0.0002 422_[+2]_62 43771 0.0002 108_[+2]_376 46222 0.00027 204_[+2]_280 44200 0.00037 103_[+2]_381 12198 0.00045 356_[+2]_128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=35 45472 ( 96) CATTTGCTTTTTGTTT 1 44259 ( 211) CTTTTGTTCTTAATTT 1 36022 ( 454) CATTCGTTTTTTTTTC 1 46271 ( 221) CCTTTGCTGTTAATTT 1 36578 ( 15) CCTTCGTTTCCCATTT 1 49135 ( 336) CATTCCTTTTTCATTC 1 11308 ( 52) GCTTTGCTTTTCTTTT 1 43764 ( 75) CTGTTGTAGTTTGTTT 1 31741 ( 206) CTCTTCTTTTTCGTTT 1 42824 ( 106) AATTTCCTCTTCTTTT 1 46537 ( 84) GAGTCCTTTTTTTTTT 1 44201 ( 457) CATTTCTTGCTCATCT 1 44889 ( 468) CTTTTGTTCTTTGCAT 1 43394 ( 457) ACTCTGTTTCTCATTC 1 49431 ( 111) CTGTTCTTCCATATTT 1 48859 ( 370) CATTCGTTCCATTTTT 1 44108 ( 446) ATTCTGTTGTTCCCTT 1 48790 ( 386) ATTTCGTAGTTTTTTC 1 41473 ( 117) CTTTTGCAGCTATTTC 1 47279 ( 12) TATTCGTTGCTTGCTT 1 45061 ( 20) AAGTTCTTTCCTCCTT 1 50523 ( 282) GTGTCCCTTCCCATTT 1 35603 ( 278) GTTTTCCATTTTTCTT 1 36928 ( 62) AACTTGTTTTTTATAT 1 50491 ( 321) CCTTCCTTTCCCACTC 1 44043 ( 305) CCGATGTTTCTACTTT 1 4918 ( 149) CATTCGCACCTTGCTC 1 33313 ( 294) GTGTTCTAGGTTATTT 1 44049 ( 62) CTTTTCTTTGCCTTAT 1 1862 ( 80) ACGTTGCTTCCTCTCT 1 48347 ( 423) TTTTTGTTTCTACTGT 1 43771 ( 109) CCGTTGCTCCGACTTT 1 46222 ( 205) ATAGTGTTGTTTATTT 1 44200 ( 104) CAGCTCATTTTCGTTC 1 12198 ( 357) ATTCCGCTTATTCCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 17460 bayes= 9.06227 E= 4.3e+000 -5 116 -63 -224 36 -9 -1177 67 -322 -208 37 122 -322 -108 -295 162 -1177 37 -1177 134 -1177 61 151 -1177 -322 37 -1177 128 -63 -1177 -1177 162 -1177 -28 22 101 -322 82 -195 85 -222 -50 -295 146 -63 50 -1177 85 36 -28 -14 -7 -1177 -9 -1177 151 -163 -208 -295 162 -1177 -9 -1177 151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 35 E= 4.3e+000 0.257143 0.542857 0.142857 0.057143 0.342857 0.228571 0.000000 0.428571 0.028571 0.057143 0.285714 0.628571 0.028571 0.114286 0.028571 0.828571 0.000000 0.314286 0.000000 0.685714 0.000000 0.371429 0.628571 0.000000 0.028571 0.314286 0.000000 0.657143 0.171429 0.000000 0.000000 0.828571 0.000000 0.200000 0.257143 0.542857 0.028571 0.428571 0.057143 0.485714 0.057143 0.171429 0.028571 0.742857 0.171429 0.342857 0.000000 0.485714 0.342857 0.200000 0.200000 0.257143 0.000000 0.228571 0.000000 0.771429 0.085714 0.057143 0.028571 0.828571 0.000000 0.228571 0.000000 0.771429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][TAC][TG]T[TC][GC][TC]T[TGC][TC]T[TC][ATCG][TC]T[TC] -------------------------------------------------------------------------------- Time 20.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 21 llr = 198 E-value = 2.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 19:199:18566 pos.-specific C 6:a:::342:1: probability G :1:9::55:534 matrix T 3::::11::::: bits 2.2 2.0 1.7 ** 1.5 *** * Relative 1.3 ***** * Entropy 1.1 ***** ** * (13.6 bits) 0.9 ***** ** * 0.7 ****** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CACGAAGGAAAA consensus T CC GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46537 276 3.11e-07 ATGGTATTCT CACGAAGGAAAG TAGGTAGGCA 43771 179 9.18e-07 TGTCAGGAGT CACGAACGAAAG CGGGTAGAAG 50491 365 2.09e-06 GGCAATCAAA CACGAATGAGAA CAAACACCTC 1862 47 3.94e-06 GTTACGAAGA CACGAATCAGAA AAGAGTGGTG 45472 331 4.45e-06 GGCGAAGACC AACGAACGAAAA ATCTCCGGCG 48859 314 6.76e-06 ACGCGAAATG TACGAAGCAAGG CAAGGTAAAT 33313 261 6.76e-06 AAACGAAAGC CACGAAGAAAAG CGTCAGGTTC 44043 487 7.28e-06 CCAAACGAAC TACGAACCAAGA CC 49431 363 2.36e-05 AAAACGGGCG CACGAAGCCGCA CTGCGTAGAC 45061 155 2.36e-05 CTGTTACAAT TGCGAAGGAAGA TCTGTAAGTC 43394 347 2.36e-05 ACAAGTCATA CACGAACGCGCA AGCCCAGAAA 41473 405 2.60e-05 ATTTCCTGAC TGCGAACGAGAG AGCTCTCCAG 4918 246 2.60e-05 CCGAACGTTG CACGATGCAGGG ATTTACCGCT 46222 308 3.04e-05 CTGGTTTCGA AACGAATGAGGG CAGGGAATTT 11308 468 3.29e-05 GCAGGTTCCA CACGAAAGCAAA ATGTCGGTTC 7629 489 3.57e-05 TCCGGACGCC CACGATGCCGAA 50523 31 3.57e-05 ACAAAGTTAT TATGAAGGAAAA ATCCGGCCAA 46271 488 4.11e-05 CTCCCTGCAG CACGCACCAAAG G 44201 111 4.44e-05 CTGTCTGGCA TACGTACGAAAA TGACATTTTT 36928 403 4.44e-05 GCACCCGTAG CACAAAGAAGAA AGTTTGAACA 42824 72 7.15e-05 ATTTGTCAAA AACAAAGCAGGA ATCGAGTAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46537 3.1e-07 275_[+3]_213 43771 9.2e-07 178_[+3]_310 50491 2.1e-06 364_[+3]_124 1862 3.9e-06 46_[+3]_442 45472 4.5e-06 330_[+3]_158 48859 6.8e-06 313_[+3]_175 33313 6.8e-06 260_[+3]_228 44043 7.3e-06 486_[+3]_2 49431 2.4e-05 362_[+3]_126 45061 2.4e-05 154_[+3]_334 43394 2.4e-05 346_[+3]_142 41473 2.6e-05 404_[+3]_84 4918 2.6e-05 245_[+3]_243 46222 3e-05 307_[+3]_181 11308 3.3e-05 467_[+3]_21 7629 3.6e-05 488_[+3] 50523 3.6e-05 30_[+3]_458 46271 4.1e-05 487_[+3]_1 44201 4.4e-05 110_[+3]_378 36928 4.4e-05 402_[+3]_86 42824 7.1e-05 71_[+3]_417 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=21 46537 ( 276) CACGAAGGAAAG 1 43771 ( 179) CACGAACGAAAG 1 50491 ( 365) CACGAATGAGAA 1 1862 ( 47) CACGAATCAGAA 1 45472 ( 331) AACGAACGAAAA 1 48859 ( 314) TACGAAGCAAGG 1 33313 ( 261) CACGAAGAAAAG 1 44043 ( 487) TACGAACCAAGA 1 49431 ( 363) CACGAAGCCGCA 1 45061 ( 155) TGCGAAGGAAGA 1 43394 ( 347) CACGAACGCGCA 1 41473 ( 405) TGCGAACGAGAG 1 4918 ( 246) CACGATGCAGGG 1 46222 ( 308) AACGAATGAGGG 1 11308 ( 468) CACGAAAGCAAA 1 7629 ( 489) CACGATGCCGAA 1 50523 ( 31) TATGAAGGAAAA 1 46271 ( 488) CACGCACCAAAG 1 44201 ( 111) TACGTACGAAAA 1 36928 ( 403) CACAAAGAAGAA 1 42824 ( 72) AACAAAGCAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17604 bayes= 10.0148 E= 2.4e+003 -90 124 -1104 8 176 -1104 -121 -1104 -1104 197 -1104 -250 -148 -1104 203 -1104 176 -235 -1104 -250 176 -1104 -1104 -150 -248 46 111 -92 -148 65 124 -1104 160 -35 -1104 -1104 98 -1104 111 -1104 122 -135 37 -1104 122 -1104 78 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 21 E= 2.4e+003 0.142857 0.571429 0.000000 0.285714 0.904762 0.000000 0.095238 0.000000 0.000000 0.952381 0.000000 0.047619 0.095238 0.000000 0.904762 0.000000 0.904762 0.047619 0.000000 0.047619 0.904762 0.000000 0.000000 0.095238 0.047619 0.333333 0.476190 0.142857 0.095238 0.380952 0.523810 0.000000 0.809524 0.190476 0.000000 0.000000 0.523810 0.000000 0.476190 0.000000 0.619048 0.095238 0.285714 0.000000 0.619048 0.000000 0.380952 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]ACGAA[GC][GC]A[AG][AG][AG] -------------------------------------------------------------------------------- Time 31.42 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31741 3.66e-05 205_[+2(6.25e-06)]_68_\ [+1(2.11e-07)]_199 42824 3.42e-05 71_[+3(7.15e-05)]_22_[+2(7.05e-06)]_\ 86_[+1(4.56e-06)]_281 46537 5.03e-07 83_[+2(7.90e-06)]_176_\ [+3(3.11e-07)]_95_[+1(8.10e-06)]_106 36928 1.59e-04 61_[+2(5.68e-05)]_325_\ [+3(4.44e-05)]_24_[+1(5.36e-06)]_50 48790 1.04e-01 385_[+2(3.32e-05)]_41_\ [+2(7.92e-05)]_42 43394 2.28e-03 86_[+2(5.68e-05)]_244_\ [+3(2.36e-05)]_98_[+2(2.05e-05)]_28 1862 6.63e-03 46_[+3(3.94e-06)]_442 43764 1.48e-04 74_[+2(2.96e-06)]_181_\ [+1(1.38e-05)]_217 33313 2.10e-05 260_[+3(6.76e-06)]_160_\ [+1(1.56e-06)]_56 44043 1.74e-05 304_[+2(7.92e-05)]_41_\ [+1(1.84e-06)]_113_[+3(7.28e-06)]_2 44049 4.75e-01 500 44108 1.18e-03 370_[+1(3.84e-06)]_53_\ [+1(8.10e-06)]_53 44200 2.10e-01 500 50523 2.75e-04 30_[+3(3.57e-05)]_145_\ [+1(1.64e-05)]_82_[+2(4.37e-05)]_203 44259 3.44e-03 210_[+2(4.65e-07)]_274 11308 1.43e-05 5_[+1(8.69e-06)]_34_[+2(2.96e-06)]_\ 400_[+3(3.29e-05)]_21 44889 5.61e-05 291_[+1(1.00e-06)]_164_\ [+2(2.05e-05)]_17 7629 2.25e-01 488_[+3(3.57e-05)] 4918 2.16e-02 245_[+3(2.60e-05)]_243 45472 1.41e-08 67_[+1(1.09e-06)]_16_[+2(8.18e-08)]_\ 219_[+3(4.45e-06)]_11_[+1(4.88e-06)]_135 12198 4.98e-01 500 46222 4.14e-02 307_[+3(3.04e-05)]_181 44201 9.08e-07 34_[+1(1.11e-05)]_22_[+1(7.12e-08)]_\ 30_[+3(4.44e-05)]_193_[+1(1.19e-05)]_129_[+2(1.23e-05)]_28 50491 6.26e-04 320_[+2(6.18e-05)]_28_\ [+3(2.09e-06)]_124 49135 1.64e-03 335_[+2(2.27e-06)]_149 48859 2.91e-07 313_[+3(6.76e-06)]_22_\ [+1(7.12e-08)]_10_[+2(2.27e-05)]_115 36578 4.75e-05 14_[+2(2.27e-06)]_36_[+1(3.84e-06)]_\ 102_[+1(4.90e-05)]_308 36022 3.97e-04 318_[+1(1.80e-05)]_123_\ [+2(1.08e-06)]_31 45061 9.78e-05 19_[+2(4.00e-05)]_119_\ [+3(2.36e-05)]_66_[+1(8.10e-06)]_256 49431 1.34e-05 110_[+2(2.27e-05)]_95_\ [+1(1.47e-06)]_73_[+1(8.25e-05)]_44_[+3(2.36e-05)]_126 41473 7.81e-03 116_[+2(3.65e-05)]_272_\ [+3(2.60e-05)]_84 47279 5.82e-02 11_[+2(4.00e-05)]_473 43771 9.46e-04 178_[+3(9.18e-07)]_310 46271 6.43e-06 220_[+2(1.71e-06)]_189_\ [+1(4.88e-06)]_50_[+3(4.11e-05)]_1 35603 1.18e-01 277_[+2(5.68e-05)]_207 48347 3.18e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************