******************************************************************************** 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/142/142.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10340 1.0000 500 10564 1.0000 500 11294 1.0000 500 11300 1.0000 500 11693 1.0000 500 1244 1.0000 500 1382 1.0000 500 15819 1.0000 500 16507 1.0000 500 18841 1.0000 500 19435 1.0000 500 1985 1.0000 500 20622 1.0000 500 21446 1.0000 500 21603 1.0000 500 22079 1.0000 500 22297 1.0000 500 22850 1.0000 500 2310 1.0000 500 23792 1.0000 500 24197 1.0000 500 25016 1.0000 500 25576 1.0000 500 25678 1.0000 500 260816 1.0000 500 262296 1.0000 500 263327 1.0000 500 263404 1.0000 500 263562 1.0000 500 268652 1.0000 500 2775 1.0000 500 30846 1.0000 500 31052 1.0000 500 32899 1.0000 500 3359 1.0000 500 34738 1.0000 500 3500 1.0000 500 36582 1.0000 500 37830 1.0000 500 4224 1.0000 500 42646 1.0000 500 4525 1.0000 500 5820 1.0000 500 7977 1.0000 500 8445 1.0000 500 bd706 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/142/142.seqs.fa -oc motifs/142 -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= 46 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= 23000 N= 46 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.221 G 0.248 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.221 G 0.248 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 43 llr = 421 E-value = 1.3e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 14:17:463:74261:74142 pos.-specific C :14::5:12133:2113:134 probability G 8348:46138:36129::6:2 matrix T :22:21:21:::216::6222 bits 2.2 2.0 1.7 1.5 * Relative 1.3 * * Entropy 1.1 * * * ** ** (14.1 bits) 0.9 * * * ** ** 0.7 * **** ** * *** 0.4 * ****** *********** 0.2 ******** ************ 0.0 --------------------- Multilevel GAGGACGAGGAAGATGATGAC consensus GC TGATA CGA CATCG sequence T C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 268652 306 2.48e-10 CTTACGATTG GGGGACGAAGAGGATGATTAC TTTGGGGCTC 5820 16 6.89e-10 GCCTCGCGAC GGCGACGACGACGATGATGAT GATGCACCAT 32899 21 1.30e-08 AGAAGCCAAT GACGAGGTAGAGAATGATGCC ACCAGTCCAG 15819 260 4.36e-08 TTTGATGGGT GGCGAGGAGGAAGGTGATACC AAGAGTCCTG 30846 270 1.11e-07 CTGTCTGTAC GACGTCGAACACGATGAAGAG TTTGTATGGT 3500 270 1.72e-07 AACGTGACCC GACGACGAGGAGGAGGAGGCA CCGCAATAAT 263404 166 3.91e-07 TGTGATTCCA GCCGTCGACGAAAATGAAGAG TGACAAACAG 42646 377 5.08e-07 TGAGTGGGGC ATCGACGAAGAGGAGGCTGAC GCCAAGAAGG 25678 171 1.36e-06 CGATGGTTTC GTTGACAGCGACGATGAAGAA TGGGATTGAC 260816 69 1.71e-06 GACGGAGAGA GATGACGTAGACGACGCAGCA GATGGAAGTG 263562 269 1.92e-06 TGGTACGAGG GAGGAGAAGGAGAGGGATGTG GAGGGTGTGT 36582 29 2.99e-06 AGCCAATGGT GATAGCGAAGAAGATGAATAC ATACTCGAGG 22850 49 3.33e-06 TTGGAGGAAG GTCTTCGAAGCAGATGATGCA TTCCACTGGT 31052 390 3.71e-06 GCCGATCGGA GTTGTCGACGCATATGATTCG GGAGCGTAGT 2775 318 5.08e-06 GCTTTTGAGC GTCGAGAAGCAGAAAGATTAC AGACAGCTGT 23792 204 5.62e-06 GAAGGATATC GACGACGAATAGGCGGATGTT GGACGAAATA bd706 131 6.88e-06 GCATTGGGGG GAGAACGAAGAGTTTGCTTTC AAAGACTAAG 8445 218 6.88e-06 CTTCGACGAA GCCATCAATGAAGATGAAGAA CGTGCGAGAT 11294 15 6.88e-06 AGAGTGGGCG GGGGTCGACGACATAGCAGCG AACATCAGCG 4525 168 7.60e-06 TGTGTTTGGG GCGAAGGGCGACGATGATGAT TTCATGGTAT 22297 86 7.60e-06 CTCTATGGTG GAGGAGGCGGCGACGGCTGCC ACTACGGTGG 263327 86 1.02e-05 GTCGTCTTTC CTGGAGGAGGAAGAGGATCTC CGTTCGTTTG 11693 54 1.12e-05 TGCGGGTGAC GTCGCCGTTGCCGTTGATGCC AACTTCTCCA 1382 326 1.35e-05 TAGCTCAACA GAGGACAATGAAGGTCAAAAG CTGCTTTCAT 25576 98 1.94e-05 CCATGGCGGT TGTGACGTTGACGTTGATGCA CCGTCTTCGA 16507 377 2.12e-05 GAACCATAAT CACGAGGAAGCCACTGATCAC TGCACCTCTC 1985 115 2.32e-05 GCGGCCGTCG GGGGAGAAGGTGGAGGAGGAG AGGTCGTAGC 22079 158 2.53e-05 AGAACAAACT GAGAACATGGCAGCTGCTAAT CTAGCTGCTG 262296 25 2.76e-05 ATGAGTTTCA GAGGATATAGCAGACGATTAT ACAAAAGGTC 1244 170 3.01e-05 ATATTAAAAA GGGGAGGAAGAGGTAGAAAGG GTTTGGAGAG 34738 328 3.27e-05 GGGCTTGCTT GGCGAGAAGGAGTCTCCATTC AAAGGATCAA 25016 286 3.27e-05 TCGTGAGCAA GGGGGGATGCAAGATGAAAAG ATTTGATAGG 19435 235 3.56e-05 CAAAATACCT GATGACAACGAAAGTAATGAT GATGGTGAGG 2310 166 4.20e-05 ATGTTGGTGA GGGATGGTGGAGGAGGACGTC TACCGATGAG 24197 23 4.94e-05 TGGTTGAGCA AGCGACATCCAATATGCTGCA ATGTGCAATA 10564 342 4.94e-05 CTTTCACGGC AGCGACGTTGCCTCTGATGCT ATGCAATATT 11300 180 5.35e-05 GTCAATGTGA GGTGTTGAGGCGGCAGCATAC TCGGTAAGAG 10340 335 5.35e-05 AAGATATTTT GAGGAGAGCGAATGTGAACTC AAGTTATATT 20622 137 7.31e-05 GTCGTCTGCG GGTGTTGCCGCCGAAGCAGCC GTCGGCAGCT 18841 90 1.06e-04 GATCATTCAA GAGGAGACGCCCATTGCATAC GATGACAAAC 3359 128 1.14e-04 GCGGTTGTGA GTTGTCGAGTAATACGATGTA CCGATACCAC 21446 304 1.32e-04 GCCTTAGTCT GAGGCAAAAGAGGATCCTTCC TTTTCTGCTG 37830 160 1.42e-04 CTACTGGTGG TGGTAGAAGGAAGAAGAAACG ATCGTCAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268652 2.5e-10 305_[+1]_174 5820 6.9e-10 15_[+1]_464 32899 1.3e-08 20_[+1]_459 15819 4.4e-08 259_[+1]_220 30846 1.1e-07 269_[+1]_210 3500 1.7e-07 269_[+1]_210 263404 3.9e-07 165_[+1]_314 42646 5.1e-07 376_[+1]_103 25678 1.4e-06 170_[+1]_309 260816 1.7e-06 68_[+1]_411 263562 1.9e-06 268_[+1]_211 36582 3e-06 28_[+1]_451 22850 3.3e-06 48_[+1]_431 31052 3.7e-06 389_[+1]_90 2775 5.1e-06 317_[+1]_162 23792 5.6e-06 203_[+1]_276 bd706 6.9e-06 130_[+1]_349 8445 6.9e-06 217_[+1]_262 11294 6.9e-06 14_[+1]_465 4525 7.6e-06 167_[+1]_312 22297 7.6e-06 85_[+1]_394 263327 1e-05 85_[+1]_394 11693 1.1e-05 53_[+1]_426 1382 1.3e-05 325_[+1]_154 25576 1.9e-05 97_[+1]_382 16507 2.1e-05 376_[+1]_103 1985 2.3e-05 114_[+1]_365 22079 2.5e-05 157_[+1]_322 262296 2.8e-05 24_[+1]_455 1244 3e-05 169_[+1]_310 34738 3.3e-05 327_[+1]_152 25016 3.3e-05 285_[+1]_194 19435 3.6e-05 234_[+1]_245 2310 4.2e-05 165_[+1]_314 24197 4.9e-05 22_[+1]_457 10564 4.9e-05 341_[+1]_138 11300 5.3e-05 179_[+1]_300 10340 5.3e-05 334_[+1]_145 20622 7.3e-05 136_[+1]_343 18841 0.00011 89_[+1]_390 3359 0.00011 127_[+1]_352 21446 0.00013 303_[+1]_176 37830 0.00014 159_[+1]_320 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=43 268652 ( 306) GGGGACGAAGAGGATGATTAC 1 5820 ( 16) GGCGACGACGACGATGATGAT 1 32899 ( 21) GACGAGGTAGAGAATGATGCC 1 15819 ( 260) GGCGAGGAGGAAGGTGATACC 1 30846 ( 270) GACGTCGAACACGATGAAGAG 1 3500 ( 270) GACGACGAGGAGGAGGAGGCA 1 263404 ( 166) GCCGTCGACGAAAATGAAGAG 1 42646 ( 377) ATCGACGAAGAGGAGGCTGAC 1 25678 ( 171) GTTGACAGCGACGATGAAGAA 1 260816 ( 69) GATGACGTAGACGACGCAGCA 1 263562 ( 269) GAGGAGAAGGAGAGGGATGTG 1 36582 ( 29) GATAGCGAAGAAGATGAATAC 1 22850 ( 49) GTCTTCGAAGCAGATGATGCA 1 31052 ( 390) GTTGTCGACGCATATGATTCG 1 2775 ( 318) GTCGAGAAGCAGAAAGATTAC 1 23792 ( 204) GACGACGAATAGGCGGATGTT 1 bd706 ( 131) GAGAACGAAGAGTTTGCTTTC 1 8445 ( 218) GCCATCAATGAAGATGAAGAA 1 11294 ( 15) GGGGTCGACGACATAGCAGCG 1 4525 ( 168) GCGAAGGGCGACGATGATGAT 1 22297 ( 86) GAGGAGGCGGCGACGGCTGCC 1 263327 ( 86) CTGGAGGAGGAAGAGGATCTC 1 11693 ( 54) GTCGCCGTTGCCGTTGATGCC 1 1382 ( 326) GAGGACAATGAAGGTCAAAAG 1 25576 ( 98) TGTGACGTTGACGTTGATGCA 1 16507 ( 377) CACGAGGAAGCCACTGATCAC 1 1985 ( 115) GGGGAGAAGGTGGAGGAGGAG 1 22079 ( 158) GAGAACATGGCAGCTGCTAAT 1 262296 ( 25) GAGGATATAGCAGACGATTAT 1 1244 ( 170) GGGGAGGAAGAGGTAGAAAGG 1 34738 ( 328) GGCGAGAAGGAGTCTCCATTC 1 25016 ( 286) GGGGGGATGCAAGATGAAAAG 1 19435 ( 235) GATGACAACGAAAGTAATGAT 1 2310 ( 166) GGGATGGTGGAGGAGGACGTC 1 24197 ( 23) AGCGACATCCAATATGCTGCA 1 10564 ( 342) AGCGACGTTGCCTCTGATGCT 1 11300 ( 180) GGTGTTGAGGCGGCAGCATAC 1 10340 ( 335) GAGGAGAGCGAATGTGAACTC 1 20622 ( 137) GGTGTTGCCGCCGAAGCAGCC 1 18841 ( 90) GAGGAGACGCCCATTGCATAC 1 3359 ( 128) GTTGTCGAGTAATACGATGTA 1 21446 ( 304) GAGGCAAAAGAGGATCCTTCC 1 37830 ( 160) TGGTAGAAGGAAGAAGAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22080 bayes= 9.33229 E= 1.3e-014 -192 -225 175 -251 58 -167 49 -51 -1207 75 75 -35 -92 -1207 171 -251 135 -225 -242 -19 -350 127 58 -193 49 -1207 134 -1207 125 -167 -183 -19 19 7 49 -119 -1207 -93 175 -251 145 21 -1207 -351 49 33 49 -1207 -34 -1207 134 -71 114 -44 -109 -93 -92 -167 -42 119 -350 -167 187 -1207 145 33 -1207 -1207 49 -325 -242 107 -92 -167 117 -19 74 66 -341 -51 -51 92 -10 -71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 43 E= 1.3e-014 0.069767 0.046512 0.837209 0.046512 0.395349 0.069767 0.348837 0.186047 0.000000 0.372093 0.418605 0.209302 0.139535 0.000000 0.813953 0.046512 0.674419 0.046512 0.046512 0.232558 0.023256 0.534884 0.372093 0.069767 0.372093 0.000000 0.627907 0.000000 0.627907 0.069767 0.069767 0.232558 0.302326 0.232558 0.348837 0.116279 0.000000 0.116279 0.837209 0.046512 0.720930 0.255814 0.000000 0.023256 0.372093 0.279070 0.348837 0.000000 0.209302 0.000000 0.627907 0.162791 0.581395 0.162791 0.116279 0.139535 0.139535 0.069767 0.186047 0.604651 0.023256 0.069767 0.906977 0.000000 0.720930 0.279070 0.000000 0.000000 0.372093 0.023256 0.046512 0.558140 0.139535 0.069767 0.558140 0.232558 0.441860 0.348837 0.023256 0.186047 0.186047 0.418605 0.232558 0.162791 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AG][GCT]G[AT][CG][GA][AT][GAC]G[AC][AGC][GA]ATG[AC][TA][GT][AC][CG] -------------------------------------------------------------------------------- Time 21.96 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 37 llr = 379 E-value = 4.0e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 14:11::12122141:3:::1 pos.-specific C :12:13:21:::1211:31:2 probability G 741621a244228149:52:5 matrix T 2:8366:54566125:72792 bits 2.2 2.0 * 1.7 * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * * ** * (14.8 bits) 0.9 * * * * ** ** 0.7 **** ** * * ** ** 0.4 **** ** **** ***** 0.2 ********************* 0.0 --------------------- Multilevel GATGTTGTTTTTGATGTGTTG consensus TG T C CGGAA CG ACG T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 22850 216 5.08e-10 AAAGCCGCTT GCTGTTGTTGTTGCTGTGTTG TGTTGCCTCC 11693 187 1.24e-08 TAGTGTTTCG TGTGTTGTGTTAGTGGTGTTG AGGGTTTGAG 263562 347 4.20e-08 TATATTTGGG GACTTTGTGTTTGAGGACTTG TGTGAGTTAT 1382 166 5.81e-08 GTCTGCGGCT GATTTCGCTGATGAGGTGTTC ATTTTGTGAG 20622 175 9.22e-08 GCTCGTCTAT GGTGTCGTTTTGGCTGTCGTT CGTCATGGCT 22297 174 1.08e-07 TCAGCTCTAT GATGGTGCTGTTGAAGTGTTC TGGAGCGTCT 18841 339 2.92e-07 CTTCCTGTGC GGTGCTGTTGGTGCGGTGGTT GGTTTGTTGT 11294 45 5.63e-07 GAACATCAGC GGTGATGCGATTGATGACTTT ATCAAGTCGT 32899 101 6.39e-07 TTTCTCTAGC GGTGTTGTTGTTGGTGTGTGT GCCGTCACTC 24197 319 6.39e-07 TAGTTGAAGT GGTGTTGTTTTGTTTGAGTTG TTGTGAAATT 262296 282 1.04e-06 ACGTTGGGTG GGTGTTGCGTTGCTTGTTTTG CGTTGCTTTG 3359 32 2.58e-06 TTGGTTGTTG TATGCCGTATAAGAGGAGTTG TCCTTATCAT 23792 56 3.55e-06 GGCTGCCATT GATGCCGGATTGGCGCTGTTG GTGGTGGTGT 37830 472 3.93e-06 GTTGTGAGTG AACGTTGGTGTTGTGCTGTTG GTGAAGTG 10564 311 4.35e-06 CCGTCCCTTC GCCTTCGGCTTTGATGTGTTC CTTTCACGGC 1244 357 4.82e-06 TTGCAGGACA TCTATTGATTTTGACGAGTTG CTTTGTAAGA 7977 176 5.87e-06 ACAGTTACGA AGGGTTGAGATTGAGGTGTTG AATCGGTATT 42646 266 7.13e-06 GAAACTTGCA GACGATGCTGATGAGGTATTG GCAAAATGCC 25678 350 7.84e-06 CGTTGGTACT GGTACCGTGTTTGATCTCTTA CCTCTACCTT 4224 109 8.62e-06 GGACAACCAA AATATTGAGTTAGCTGTTTTT CGGGTTACCA 1985 189 8.62e-06 TTTGTGTGTA GGTAGGGGGGTTGCGGTCGTC GTCGGCTGTC 3500 443 1.24e-05 GTTGAAAGCG GATGATGTAGGTGCAGACGTG GTTACATCTG 34738 42 1.48e-05 CAACTACTGT TGTATCGTGTAGGATCTTTTG TTAACACCTG 4525 213 1.62e-05 AAGGGTCGGT GATTGGGTGAAAGAGGTGGTT CGGTGGGGGG 21446 358 1.62e-05 AGGAAGGCCA TATTTGGACGATGTTGTGTTG GTGGAAAGGC 8445 371 1.76e-05 AACTTATGGT GAGGTCGTTTTTGGTGTTCTT GTTGCCGTTG 25016 260 1.76e-05 TGCCGTGATG GGTGTTGGGTGTAGTCTCGTG AGCAAGGGGG 30846 303 1.92e-05 TGTATGGTGG AGTGTTGCTGTTGCGGATTCG AGCTCCGCTT 263404 299 2.08e-05 AATTGTTAGA GGTGAGGGAGAAGATGTGCTG CAATAGTCGA 21603 346 2.46e-05 TATATCACTT TATTTCGTTTTATGGGAGTTC TATTTTCCTC 268652 57 3.13e-05 CAGTGTTTCT GCTTGTGTATATCACGTCTTT ACACAGCTTC 25576 269 4.25e-05 CCACTCGTCA TGTTGTGTGGAAGCCGACGTT CGATGCCTAA 2310 216 5.31e-05 CCATTGAGGT GATGATGCTTTGAGCGATTTG GCTATGGCGT 263327 43 5.71e-05 TCTCATCGTT GGCGTCGTGTTCATTGTCGTC GTGTTCATTG 11300 268 8.66e-05 CAAAGAACAC GATGGTGCACGTCTTGTCTTC CTCGTCCTTG bd706 93 9.26e-05 GTATGTAGAT GCTTTTGGGGGAGAAGAGGTA CAGTCTGGCA 2775 127 1.73e-04 TGATTGTTCG TACTCGGATAGAGATGTGTTC TCGGCTAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22850 5.1e-10 215_[+2]_264 11693 1.2e-08 186_[+2]_293 263562 4.2e-08 346_[+2]_133 1382 5.8e-08 165_[+2]_314 20622 9.2e-08 174_[+2]_305 22297 1.1e-07 173_[+2]_306 18841 2.9e-07 338_[+2]_141 11294 5.6e-07 44_[+2]_435 32899 6.4e-07 100_[+2]_379 24197 6.4e-07 318_[+2]_161 262296 1e-06 281_[+2]_198 3359 2.6e-06 31_[+2]_448 23792 3.5e-06 55_[+2]_424 37830 3.9e-06 471_[+2]_8 10564 4.4e-06 310_[+2]_169 1244 4.8e-06 356_[+2]_123 7977 5.9e-06 175_[+2]_304 42646 7.1e-06 265_[+2]_214 25678 7.8e-06 349_[+2]_130 4224 8.6e-06 108_[+2]_371 1985 8.6e-06 188_[+2]_291 3500 1.2e-05 442_[+2]_37 34738 1.5e-05 41_[+2]_438 4525 1.6e-05 212_[+2]_267 21446 1.6e-05 357_[+2]_122 8445 1.8e-05 370_[+2]_109 25016 1.8e-05 259_[+2]_220 30846 1.9e-05 302_[+2]_177 263404 2.1e-05 298_[+2]_181 21603 2.5e-05 345_[+2]_134 268652 3.1e-05 56_[+2]_423 25576 4.3e-05 268_[+2]_211 2310 5.3e-05 215_[+2]_264 263327 5.7e-05 42_[+2]_437 11300 8.7e-05 267_[+2]_212 bd706 9.3e-05 92_[+2]_387 2775 0.00017 126_[+2]_353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=37 22850 ( 216) GCTGTTGTTGTTGCTGTGTTG 1 11693 ( 187) TGTGTTGTGTTAGTGGTGTTG 1 263562 ( 347) GACTTTGTGTTTGAGGACTTG 1 1382 ( 166) GATTTCGCTGATGAGGTGTTC 1 20622 ( 175) GGTGTCGTTTTGGCTGTCGTT 1 22297 ( 174) GATGGTGCTGTTGAAGTGTTC 1 18841 ( 339) GGTGCTGTTGGTGCGGTGGTT 1 11294 ( 45) GGTGATGCGATTGATGACTTT 1 32899 ( 101) GGTGTTGTTGTTGGTGTGTGT 1 24197 ( 319) GGTGTTGTTTTGTTTGAGTTG 1 262296 ( 282) GGTGTTGCGTTGCTTGTTTTG 1 3359 ( 32) TATGCCGTATAAGAGGAGTTG 1 23792 ( 56) GATGCCGGATTGGCGCTGTTG 1 37830 ( 472) AACGTTGGTGTTGTGCTGTTG 1 10564 ( 311) GCCTTCGGCTTTGATGTGTTC 1 1244 ( 357) TCTATTGATTTTGACGAGTTG 1 7977 ( 176) AGGGTTGAGATTGAGGTGTTG 1 42646 ( 266) GACGATGCTGATGAGGTATTG 1 25678 ( 350) GGTACCGTGTTTGATCTCTTA 1 4224 ( 109) AATATTGAGTTAGCTGTTTTT 1 1985 ( 189) GGTAGGGGGGTTGCGGTCGTC 1 3500 ( 443) GATGATGTAGGTGCAGACGTG 1 34738 ( 42) TGTATCGTGTAGGATCTTTTG 1 4525 ( 213) GATTGGGTGAAAGAGGTGGTT 1 21446 ( 358) TATTTGGACGATGTTGTGTTG 1 8445 ( 371) GAGGTCGTTTTTGGTGTTCTT 1 25016 ( 260) GGTGTTGGGTGTAGTCTCGTG 1 30846 ( 303) AGTGTTGCTGTTGCGGATTCG 1 263404 ( 299) GGTGAGGGAGAAGATGTGCTG 1 21603 ( 346) TATTTCGTTTTATGGGAGTTC 1 268652 ( 57) GCTTGTGTATATCACGTCTTT 1 25576 ( 269) TGTTGTGTGGAAGCCGACGTT 1 2310 ( 216) GATGATGCTTTGAGCGATTTG 1 263327 ( 43) GGCGTCGTGTTCATTGTCGTC 1 11300 ( 268) GATGGTGCACGTCTTGTCTTC 1 bd706 ( 93) GCTTTTGGGGGAGAAGAGGTA 1 2775 ( 127) TACTCGGATAGAGATGTGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22080 bayes= 9.3839 E= 4.0e-010 -129 -1185 144 -30 71 -71 80 -1185 -1185 -45 -220 156 -97 -1185 126 2 -97 -71 -62 109 -1185 29 -88 116 -1185 -1185 201 -1185 -97 -3 -39 79 -70 -203 61 61 -129 -303 61 87 -12 -1185 -62 116 -12 -303 -62 109 -170 -145 166 -230 71 14 -88 -49 -170 -103 50 79 -1185 -71 180 -1185 17 -1185 -1185 140 -329 42 105 -71 -1185 -203 -3 140 -1185 -303 -320 183 -229 -3 97 -13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 37 E= 4.0e-010 0.108108 0.000000 0.675676 0.216216 0.432432 0.135135 0.432432 0.000000 0.000000 0.162162 0.054054 0.783784 0.135135 0.000000 0.594595 0.270270 0.135135 0.135135 0.162162 0.567568 0.000000 0.270270 0.135135 0.594595 0.000000 0.000000 1.000000 0.000000 0.135135 0.216216 0.189189 0.459459 0.162162 0.054054 0.378378 0.405405 0.108108 0.027027 0.378378 0.486486 0.243243 0.000000 0.162162 0.594595 0.243243 0.027027 0.162162 0.567568 0.081081 0.081081 0.783784 0.054054 0.432432 0.243243 0.135135 0.189189 0.081081 0.108108 0.351351 0.459459 0.000000 0.135135 0.864865 0.000000 0.297297 0.000000 0.000000 0.702703 0.027027 0.297297 0.513514 0.162162 0.000000 0.054054 0.243243 0.702703 0.000000 0.027027 0.027027 0.945946 0.054054 0.216216 0.486486 0.243243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][AG]T[GT]T[TC]G[TC][TG][TG][TA][TA]G[AC][TG]G[TA][GC][TG]T[GTC] -------------------------------------------------------------------------------- Time 42.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 22 llr = 270 E-value = 1.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1:::1:11::::12:2:51 pos.-specific C a2427248365765756:726 probability G :1:3::::2:13112::3:13 matrix T :7553852434:34:34522: bits 2.2 * 2.0 * 1.7 * 1.5 * * Relative 1.3 * ** * * Entropy 1.1 * ** * * * (17.7 bits) 0.9 * ** * * ** * * * * 0.7 *** **** ****** * * * 0.4 ******** ********** * 0.2 ********************* 0.0 --------------------- Multilevel CTTTCTTCTCCCCCCCCTCAC consensus CGT C CTTGTT TTG TG sequence C G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11300 118 7.85e-09 CGAAACAAAA CTTCCTCCCACCCTCCCTCCC TCCTACCTGC 3500 217 1.44e-08 GGAGGTGCAC CTCGCCCCTCGCCCCTCTCAC CTCCATTCTC 1244 202 7.33e-08 TTTGGAGAGC CTTTTTACCCTCCTCCTTCTC CAGAAGGGGA 262296 465 1.06e-07 GTTGTGGCTG CTTCCTCTTCTCCCCCTTCAA AAACCCTGAC 10340 21 1.51e-07 TCTTCCATTT CCATCCTCCCTGCTCCCTCAC TCATCACGAT 34738 73 1.69e-07 TTAACACCTG CCTTCTTCTCTCTGCACACAC AGCTTGTCTA 20622 453 3.28e-07 TTCGTCACGC CTATCTTCGCCCCTCCCGTCG CCCGCCCACC 42646 223 4.48e-07 CAACAATATT CTCGTTTTGCCGCCCTTTCTC TACCACACAG 11693 118 6.06e-07 GGAGTTGGCG CCCCCTCCGCCGCCGCCGCTG CTGCCGGTGA 263562 447 8.11e-07 GCTACTTCGA CTTGTTTCTACCGCCATTCAC TGGTAATATG 18841 383 8.92e-07 AGAAACGAGC CGTGCTCCGCCCCCCGCGCGC GCCGCTCCGT 16507 315 1.18e-06 GCATCACCCG CTCTTTCCCTTCTCATCACCC CCATGTTACA 1382 365 1.18e-06 ATAGTGGCCA CTTCCTCCACCCCGCCCGTCG ACGTCGATCG 31052 215 1.41e-06 CTTCTTTCTT CATTCTTCACCCTTCACTTAC TGTTCGCAGA 21603 116 1.41e-06 CGACCGACGA CTCTTCTCCTGCTTCCTACAC TTGATTTATT 25016 154 1.68e-06 GTATTTATTT CTTCTTTCTTTCGTCCTTCAA TCAATCACCT 268652 87 2.78e-06 TACACAGCTT CGTTCCCTCTCGCTCCTTCTC TATTGACCGT 4224 69 3.02e-06 AAAGGATTCT CTCGCTACTTTCTTTTTTCAC TCCAAAGTTG 22850 260 3.02e-06 TCCAACCGAC CCTTCTTCGTCGCCGTCGAAC ACTTCAGAGT 32899 440 3.53e-06 CTCTCGAAGT CTCTCTCTCCTCTCAACACTG TCAATCCGAA 22079 410 3.53e-06 CAGGTGTGCT CTCGCTTCTCCGTCGTCAGAG GCGAGTAAAT 22297 218 4.13e-06 TTGTAGAACA CTTGCTTCTTTGCCGTCGTGG AGGTTGGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11300 7.9e-09 117_[+3]_362 3500 1.4e-08 216_[+3]_263 1244 7.3e-08 201_[+3]_278 262296 1.1e-07 464_[+3]_15 10340 1.5e-07 20_[+3]_459 34738 1.7e-07 72_[+3]_407 20622 3.3e-07 452_[+3]_27 42646 4.5e-07 222_[+3]_257 11693 6.1e-07 117_[+3]_362 263562 8.1e-07 446_[+3]_33 18841 8.9e-07 382_[+3]_97 16507 1.2e-06 314_[+3]_165 1382 1.2e-06 364_[+3]_115 31052 1.4e-06 214_[+3]_265 21603 1.4e-06 115_[+3]_364 25016 1.7e-06 153_[+3]_326 268652 2.8e-06 86_[+3]_393 4224 3e-06 68_[+3]_411 22850 3e-06 259_[+3]_220 32899 3.5e-06 439_[+3]_40 22079 3.5e-06 409_[+3]_70 22297 4.1e-06 217_[+3]_262 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=22 11300 ( 118) CTTCCTCCCACCCTCCCTCCC 1 3500 ( 217) CTCGCCCCTCGCCCCTCTCAC 1 1244 ( 202) CTTTTTACCCTCCTCCTTCTC 1 262296 ( 465) CTTCCTCTTCTCCCCCTTCAA 1 10340 ( 21) CCATCCTCCCTGCTCCCTCAC 1 34738 ( 73) CCTTCTTCTCTCTGCACACAC 1 20622 ( 453) CTATCTTCGCCCCTCCCGTCG 1 42646 ( 223) CTCGTTTTGCCGCCCTTTCTC 1 11693 ( 118) CCCCCTCCGCCGCCGCCGCTG 1 263562 ( 447) CTTGTTTCTACCGCCATTCAC 1 18841 ( 383) CGTGCTCCGCCCCCCGCGCGC 1 16507 ( 315) CTCTTTCCCTTCTCATCACCC 1 1382 ( 365) CTTCCTCCACCCCGCCCGTCG 1 31052 ( 215) CATTCTTCACCCTTCACTTAC 1 21603 ( 116) CTCTTCTCCTGCTTCCTACAC 1 25016 ( 154) CTTCTTTCTTTCGTCCTTCAA 1 268652 ( 87) CGTTCCCTCTCGCTCCTTCTC 1 4224 ( 69) CTCGCTACTTTCTTTTTTCAC 1 22850 ( 260) CCTTCTTCGTCGCCGTCGAAC 1 32899 ( 440) CTCTCTCTCCTCTCAACACTG 1 22079 ( 410) CTCGCTTCTCCGTCGTCAGAG 1 22297 ( 218) CTTGCTTCTTTGCCGTCGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22080 bayes= 10.9968 E= 1.0e-003 -1110 217 -1110 -1110 -254 -28 -145 136 -154 72 -1110 104 -1110 4 36 77 -1110 171 -1110 4 -1110 -28 -1110 162 -154 88 -1110 91 -1110 188 -1110 -55 -154 52 -13 45 -154 142 -1110 26 -1110 117 -145 62 -1110 162 36 -1110 -1110 142 -145 26 -1110 117 -145 62 -154 162 -45 -255 -54 104 -245 26 -1110 152 -1110 45 -22 -1110 13 91 -254 171 -245 -55 92 -28 -145 -23 -154 152 13 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 10.0e-004 0.000000 1.000000 0.000000 0.000000 0.045455 0.181818 0.090909 0.681818 0.090909 0.363636 0.000000 0.545455 0.000000 0.227273 0.318182 0.454545 0.000000 0.727273 0.000000 0.272727 0.000000 0.181818 0.000000 0.818182 0.090909 0.409091 0.000000 0.500000 0.000000 0.818182 0.000000 0.181818 0.090909 0.318182 0.227273 0.363636 0.090909 0.590909 0.000000 0.318182 0.000000 0.500000 0.090909 0.409091 0.000000 0.681818 0.318182 0.000000 0.000000 0.590909 0.090909 0.318182 0.000000 0.500000 0.090909 0.409091 0.090909 0.681818 0.181818 0.045455 0.181818 0.454545 0.045455 0.318182 0.000000 0.636364 0.000000 0.363636 0.227273 0.000000 0.272727 0.500000 0.045455 0.727273 0.045455 0.181818 0.500000 0.181818 0.090909 0.227273 0.090909 0.636364 0.272727 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CT[TC][TGC][CT]T[TC]C[TCG][CT][CT][CG][CT][CT]C[CT][CT][TGA]C[AT][CG] -------------------------------------------------------------------------------- Time 63.00 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10340 5.96e-05 20_[+3(1.51e-07)]_293_\ [+1(5.35e-05)]_145 10564 1.25e-03 310_[+2(4.35e-06)]_10_\ [+1(4.94e-05)]_138 11294 8.05e-06 14_[+1(6.88e-06)]_9_[+2(5.63e-07)]_\ 435 11300 8.09e-07 117_[+3(7.85e-09)]_41_\ [+1(5.35e-05)]_79_[+3(7.52e-05)]_200 11693 3.25e-09 53_[+1(1.12e-05)]_43_[+3(6.06e-07)]_\ 48_[+2(1.24e-08)]_31_[+2(3.34e-07)]_241 1244 2.72e-07 169_[+1(3.01e-05)]_11_\ [+3(7.33e-08)]_134_[+2(4.82e-06)]_123 1382 2.94e-08 49_[+3(9.85e-05)]_95_[+2(5.81e-08)]_\ 139_[+1(1.35e-05)]_18_[+3(1.18e-06)]_115 15819 9.40e-04 259_[+1(4.36e-08)]_190_\ [+1(2.12e-05)]_9 16507 2.47e-04 314_[+3(1.18e-06)]_41_\ [+1(2.12e-05)]_103 18841 6.37e-07 338_[+2(2.92e-07)]_23_\ [+3(8.92e-07)]_97 19435 1.33e-01 234_[+1(3.56e-05)]_245 1985 2.74e-03 114_[+1(2.32e-05)]_53_\ [+2(8.62e-06)]_291 20622 6.45e-08 136_[+1(7.31e-05)]_17_\ [+2(9.22e-08)]_257_[+3(3.28e-07)]_27 21446 1.26e-03 319_[+3(7.83e-05)]_17_\ [+2(1.62e-05)]_122 21603 6.29e-04 115_[+3(1.41e-06)]_209_\ [+2(2.46e-05)]_134 22079 1.14e-03 157_[+1(2.53e-05)]_231_\ [+3(3.53e-06)]_70 22297 9.62e-08 85_[+1(7.60e-06)]_67_[+2(1.08e-07)]_\ 23_[+3(4.13e-06)]_262 22850 2.41e-10 48_[+1(3.33e-06)]_146_\ [+2(5.08e-10)]_23_[+3(3.02e-06)]_220 2310 1.46e-02 165_[+1(4.20e-05)]_29_\ [+2(5.31e-05)]_264 23792 3.84e-04 55_[+2(3.55e-06)]_102_\ [+1(6.77e-05)]_4_[+1(5.62e-06)]_276 24197 1.48e-04 22_[+1(4.94e-05)]_275_\ [+2(6.39e-07)]_161 25016 1.55e-05 153_[+3(1.68e-06)]_85_\ [+2(1.76e-05)]_5_[+1(3.27e-05)]_194 25576 4.53e-04 97_[+1(1.94e-05)]_150_\ [+2(4.25e-05)]_190_[+3(5.84e-05)] 25678 6.69e-05 170_[+1(1.36e-06)]_158_\ [+2(7.84e-06)]_130 260816 4.95e-03 68_[+1(1.71e-06)]_411 262296 8.73e-08 24_[+1(2.76e-05)]_236_\ [+2(1.04e-06)]_162_[+3(1.06e-07)]_15 263327 5.11e-03 42_[+2(5.71e-05)]_22_[+1(1.02e-05)]_\ 394 263404 4.94e-05 165_[+1(3.91e-07)]_112_\ [+2(2.08e-05)]_181 263562 2.57e-09 268_[+1(1.92e-06)]_57_\ [+2(4.20e-08)]_79_[+3(8.11e-07)]_33 268652 9.14e-10 56_[+2(3.13e-05)]_9_[+3(2.78e-06)]_\ 198_[+1(2.48e-10)]_174 2775 1.66e-03 317_[+1(5.08e-06)]_162 30846 2.18e-05 15_[+1(6.77e-05)]_118_\ [+1(8.51e-05)]_94_[+1(1.11e-07)]_12_[+2(1.92e-05)]_177 31052 4.40e-05 214_[+3(1.41e-06)]_154_\ [+1(3.71e-06)]_90 32899 1.23e-09 20_[+1(1.30e-08)]_59_[+2(6.39e-07)]_\ 318_[+3(3.53e-06)]_40 3359 3.13e-03 31_[+2(2.58e-06)]_448 34738 1.72e-06 41_[+2(1.48e-05)]_10_[+3(1.69e-07)]_\ 234_[+1(3.27e-05)]_152 3500 1.27e-09 216_[+3(1.44e-08)]_32_\ [+1(1.72e-07)]_140_[+1(1.12e-05)]_49 36582 2.73e-02 28_[+1(2.99e-06)]_451 37830 3.76e-03 471_[+2(3.93e-06)]_8 4224 5.08e-04 68_[+3(3.02e-06)]_19_[+2(8.62e-06)]_\ 371 42646 4.94e-08 92_[+1(5.79e-05)]_109_\ [+3(4.48e-07)]_22_[+2(7.13e-06)]_63_[+1(2.12e-05)]_6_[+1(5.08e-07)]_103 4525 1.86e-03 167_[+1(7.60e-06)]_24_\ [+2(1.62e-05)]_267 5820 3.94e-06 15_[+1(6.89e-10)]_464 7977 4.41e-02 175_[+2(5.87e-06)]_304 8445 1.59e-03 217_[+1(6.88e-06)]_132_\ [+2(1.76e-05)]_109 bd706 2.22e-03 92_[+2(9.26e-05)]_17_[+1(6.88e-06)]_\ 349 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************