******************************************************************************** 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/449/449.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10381 1.0000 500 11869 1.0000 500 11902 1.0000 500 11966 1.0000 500 12172 1.0000 500 18434 1.0000 500 22258 1.0000 500 22916 1.0000 500 2314 1.0000 500 23952 1.0000 500 2495 1.0000 500 261754 1.0000 500 262764 1.0000 500 263089 1.0000 500 264058 1.0000 500 264725 1.0000 500 26536 1.0000 500 269100 1.0000 500 33092 1.0000 500 3751 1.0000 500 37942 1.0000 500 38726 1.0000 500 41637 1.0000 500 4287 1.0000 500 4338 1.0000 500 4708 1.0000 500 4908 1.0000 500 5010 1.0000 500 5858 1.0000 500 6541 1.0000 500 7978 1.0000 500 8576 1.0000 500 8643 1.0000 500 9491 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/449/449.seqs.fa -oc motifs/449 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.233 G 0.239 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.233 G 0.239 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 34 llr = 336 E-value = 1.1e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 13331131:2111:1112212 pos.-specific C :1::2::114::2::3::4:: probability G 726419139243:86225:74 matrix T 24:36:66:256813473414 bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 * * * Entropy 1.1 * * ** (14.3 bits) 0.8 * * ** * *** * * 0.6 * * ** * ***** * * 0.4 * * ***** ***** ** ** 0.2 ********* *********** 0.0 --------------------- Multilevel GTGGTGTTGCTTTGGTTGCGT consensus AATC AG GGG TCGTT G sequence A A G AA A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38726 230 1.12e-09 GATGTCTGTA GTGGTGTGGCGTCGGTTGTGG TCAAGCTTTG 264058 173 1.02e-07 GTAGCATTCA GTGGCGTGGCTTTGTCTGTTT CCTTCTCTGA 4287 445 1.59e-07 CCGACCACCC GTGGTGATGCTGCGGTGTCGG AAACTGCCGC 22916 356 2.43e-07 GTTGTTGAAG GCGACGTTGCGGTGGGTTTGA GCGCTCTTGG 4338 301 2.79e-07 AGGAGGAAAG GGGTTGAGGGGTTGGATTCGG CAGGATTGTA 37942 64 5.39e-07 CTACCCCTTG TTGGTATGGGTTTGGTTTTGG CTTGTTGTGT 23952 46 6.12e-07 CATGACGATG AAGTTGTTGATGTGTGTGTGT AATACATAGC 4908 416 6.93e-07 GCCATTGTCT TGAGTGTTGCGTTGGTTGATG TGTTGGATTA 33092 203 7.84e-07 TTGAGGGTGG GGAGCGTGGGTGTGGTGGTGA TTGAGACTCA 9491 40 1.27e-06 TGGCAAACTT GTATTGTAGCTGTGTTTATGT AGAGCCCACT 261754 466 1.60e-06 TCCACTCAAA GAAATGTTGCTTTGACTTCAT AGAGCACTAA 262764 454 2.00e-06 AAATCAGAGA GGAGGGTCGAGTTGGTTGCGG CATCGTCGGC 263089 430 2.23e-06 GGAGAGTTGC GTGGTGATGAGGTTGGTGCTA GTGCTGCTGC 264725 211 2.49e-06 TTGCCGCGGT GTGGCGAGGGTGTGGTGAAGA ACTGCCGAAG 5858 223 2.78e-06 GACGACGGCG GCAGGGTTGTGTTTGTTGTGT TTTGTTCGTT 2314 250 3.82e-06 TTGTTTACTG GTGGCGTGGCTGTTGTTTGGG AGGGTCGGTC 6541 30 4.69e-06 CGTCTAGGAG GAGGTGGTGTTTTGTGGATGG GGTTGTTGGT 11902 175 7.70e-06 ACAGTTGAAT GTGCTGTGGTGTTGAGTGCTT TCCGCTTTCC 22258 199 8.48e-06 TCTGGTTTGG GTGATATTGGATTGGCAGAGG AGCCACTGTT 8643 150 9.32e-06 AACGCATCGG TCATTATTGATTTGGCTTTGT TTTCCTCCTC 10381 180 1.35e-05 GGGGGAAAGC TGAGTAATGATTTGTTTGAGG TTGTGAGCCG 269100 256 1.76e-05 ATCAAAAGTT GAAACGTTGCATTGGAAACGT TGACGAACAA 2495 295 1.76e-05 GAGTGTATGC GTGTTGTTGTTTTATGTGCAA TAGCAAGCCG 5010 305 2.93e-05 TACAACCAAA GAAACGGGGGGTTGGCTATTT GAGTTGGAGG 11869 68 3.45e-05 CGCTTCTTAA GTATTGATGTTGCGTTAACGA AAGTTACAAC 11966 420 5.51e-05 AGGGACGGCT GAGGTGTGGAAGATTCTTCGT GGACCTTTCA 4708 353 5.94e-05 GAACCTTTTC GTGTTGTTGGAACGGTTAAAT TTTGTATTGA 26536 54 6.89e-05 TGCCTTCAAG GTGTAGAAGCTTTGGGGTCAG TCTACTGTCA 41637 355 7.41e-05 TGACAGCGTC TCGTCGACGCGTTTGCTTCGA ACGCCGCCGA 3751 192 7.41e-05 GCTAATATTC AAGATGTTCAGGCGACTGTGA TATCAGCCTC 7978 262 1.13e-04 ACGGCGAAGG GGGTGGTGGCGTAGAAGGAGG GTGGCTTCGA 18434 203 1.29e-04 CAAAACACGT TTGATCTTCGGTTGTATGAGT ATGCAGAACA 12172 307 2.03e-04 TGCTACAGAG AAGAAGATGCGACGAGTGCGT ACTTAATCAG 8576 382 3.09e-04 TTGACTTTAC AACATGATCTTTTGTCGGTGT GTACGTCTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38726 1.1e-09 229_[+1]_250 264058 1e-07 172_[+1]_307 4287 1.6e-07 444_[+1]_35 22916 2.4e-07 355_[+1]_124 4338 2.8e-07 300_[+1]_179 37942 5.4e-07 63_[+1]_416 23952 6.1e-07 45_[+1]_434 4908 6.9e-07 415_[+1]_64 33092 7.8e-07 202_[+1]_277 9491 1.3e-06 39_[+1]_440 261754 1.6e-06 465_[+1]_14 262764 2e-06 453_[+1]_26 263089 2.2e-06 429_[+1]_50 264725 2.5e-06 210_[+1]_269 5858 2.8e-06 222_[+1]_257 2314 3.8e-06 249_[+1]_230 6541 4.7e-06 29_[+1]_450 11902 7.7e-06 174_[+1]_305 22258 8.5e-06 198_[+1]_281 8643 9.3e-06 149_[+1]_330 10381 1.3e-05 179_[+1]_300 269100 1.8e-05 255_[+1]_224 2495 1.8e-05 294_[+1]_185 5010 2.9e-05 304_[+1]_175 11869 3.5e-05 67_[+1]_412 11966 5.5e-05 419_[+1]_60 4708 5.9e-05 352_[+1]_127 26536 6.9e-05 53_[+1]_426 41637 7.4e-05 354_[+1]_125 3751 7.4e-05 191_[+1]_288 7978 0.00011 261_[+1]_218 18434 0.00013 202_[+1]_277 12172 0.0002 306_[+1]_173 8576 0.00031 381_[+1]_98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=34 38726 ( 230) GTGGTGTGGCGTCGGTTGTGG 1 264058 ( 173) GTGGCGTGGCTTTGTCTGTTT 1 4287 ( 445) GTGGTGATGCTGCGGTGTCGG 1 22916 ( 356) GCGACGTTGCGGTGGGTTTGA 1 4338 ( 301) GGGTTGAGGGGTTGGATTCGG 1 37942 ( 64) TTGGTATGGGTTTGGTTTTGG 1 23952 ( 46) AAGTTGTTGATGTGTGTGTGT 1 4908 ( 416) TGAGTGTTGCGTTGGTTGATG 1 33092 ( 203) GGAGCGTGGGTGTGGTGGTGA 1 9491 ( 40) GTATTGTAGCTGTGTTTATGT 1 261754 ( 466) GAAATGTTGCTTTGACTTCAT 1 262764 ( 454) GGAGGGTCGAGTTGGTTGCGG 1 263089 ( 430) GTGGTGATGAGGTTGGTGCTA 1 264725 ( 211) GTGGCGAGGGTGTGGTGAAGA 1 5858 ( 223) GCAGGGTTGTGTTTGTTGTGT 1 2314 ( 250) GTGGCGTGGCTGTTGTTTGGG 1 6541 ( 30) GAGGTGGTGTTTTGTGGATGG 1 11902 ( 175) GTGCTGTGGTGTTGAGTGCTT 1 22258 ( 199) GTGATATTGGATTGGCAGAGG 1 8643 ( 150) TCATTATTGATTTGGCTTTGT 1 10381 ( 180) TGAGTAATGATTTGTTTGAGG 1 269100 ( 256) GAAACGTTGCATTGGAAACGT 1 2495 ( 295) GTGTTGTTGTTTTATGTGCAA 1 5010 ( 305) GAAACGGGGGGTTGGCTATTT 1 11869 ( 68) GTATTGATGTTGCGTTAACGA 1 11966 ( 420) GAGGTGTGGAAGATTCTTCGT 1 4708 ( 353) GTGTTGTTGGAACGGTTAAAT 1 26536 ( 54) GTGTAGAAGCTTTGGGGTCAG 1 41637 ( 355) TCGTCGACGCGTTTGCTTCGA 1 3751 ( 192) AAGATGTTCAGGCGACTGTGA 1 7978 ( 262) GGGTGGTGGCGTAGAAGGAGG 1 18434 ( 203) TTGATCTTCGGTTGTATGAGT 1 12172 ( 307) AAGAAGATGCGACGAGTGCGT 1 8576 ( 382) AACATGATCTTTTGTCGGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 8.97356 E= 1.1e-009 -115 -1173 156 -60 2 -98 -44 73 31 -298 144 -1173 2 -298 78 14 -215 1 -144 121 -115 -298 184 -1173 17 -1173 -202 128 -215 -198 44 107 -1173 -140 193 -1173 -34 72 -2 -60 -115 -1173 78 82 -215 -1173 44 121 -215 -40 -1173 152 -315 -1173 178 -86 -83 -1173 123 14 -115 18 -2 52 -157 -1173 -22 140 -34 -1173 106 14 -34 72 -302 52 -115 -1173 162 -86 -15 -1173 56 63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 34 E= 1.1e-009 0.117647 0.000000 0.705882 0.176471 0.264706 0.117647 0.176471 0.441176 0.323529 0.029412 0.647059 0.000000 0.264706 0.029412 0.411765 0.294118 0.058824 0.235294 0.088235 0.617647 0.117647 0.029412 0.852941 0.000000 0.294118 0.000000 0.058824 0.647059 0.058824 0.058824 0.323529 0.558824 0.000000 0.088235 0.911765 0.000000 0.205882 0.382353 0.235294 0.176471 0.117647 0.000000 0.411765 0.470588 0.058824 0.000000 0.323529 0.617647 0.058824 0.176471 0.000000 0.764706 0.029412 0.000000 0.823529 0.147059 0.147059 0.000000 0.558824 0.294118 0.117647 0.264706 0.235294 0.382353 0.088235 0.000000 0.205882 0.705882 0.205882 0.000000 0.500000 0.294118 0.205882 0.382353 0.029412 0.382353 0.117647 0.000000 0.735294 0.147059 0.235294 0.000000 0.352941 0.411765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[TA][GA][GTA][TC]G[TA][TG]G[CGA][TG][TG]TG[GT][TCG][TG][GTA][CTA]G[TGA] -------------------------------------------------------------------------------- Time 10.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 17 llr = 219 E-value = 1.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2194251485:45:45426:2 pos.-specific C 5916548514a1:93226391 probability G 1:::41:112:521233::1: matrix T 2::::11:::::2:1:211:6 bits 2.1 * 1.9 * 1.7 * * * 1.5 ** * * * Relative 1.3 ** * * * * Entropy 1.1 *** * * * * * (18.6 bits) 0.8 *** * * ** * * * 0.6 **** ****** * **** 0.4 ************** * **** 0.2 **************** **** 0.0 --------------------- Multilevel CCACCACCAACGACAAACACT consensus T AGC A C AG CGGAC A sequence T GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 4908 46 2.57e-09 AGCCTGAGGC CCACCTCCACCGACAGTCACT GACGACTCAT 8643 252 1.82e-08 AGTAACGAGA CCACCAAAACCGTCCAGCACT GGGACGCTCT 264058 392 3.47e-08 ATGTTACAAA CCACCACGAGCAACGAGCACA ACGCAACGAG 12172 470 9.88e-08 CCACATCAAT ACACCAACAACGACGGACACA TCCCGAAATC 18434 428 1.10e-07 GTGTGCCCCG ACACACCCAGCGGCAGCCACT CTACTTCACT 4338 25 1.86e-07 CGTACAACAT CCACCACCACCATCCCTACCA CTTCCCTTCA 261754 436 2.05e-07 TGTCAGAAGA CCACCACAGACGTCGAACAGT CCACTCAAAG 7978 52 2.75e-07 GCCAAAAAGA TCAACGCCACCGGCAGGAACT TCATACACTT 33092 62 6.24e-07 CAACTCCTCG TCACGACCCACAACAAATCCT TCTGGGTCGT 263089 253 8.04e-07 GCACCGATCA TCAAGCCGAACAACGCCACCT GGGCGATCAG 11869 163 8.73e-07 AAACTACTCT TCACGTCCAACAACTCCACCT TAAGAATGTT 26536 264 1.11e-06 CGGAGCAGAC CCCAGCCCAACGACTAGCTCC TGTGGAAGGG 4708 436 1.52e-06 CGTTCACAGT GCAAACCAAACAAGCAACACT TTTTGTTACT 38726 3 1.63e-06 GC ACAAACTAAACAACAAGCACA GATTCAGCAG 11902 418 2.04e-06 CGAGGCCACC CCAACACCGCCCTCCATCTCT CAACCTTCCC 9491 437 2.19e-06 AAGGTAGGCA CAAAGCCAAGCGGCACACACC TATCACTGGA 4287 5 3.31e-06 CCCG CCCCGACAACCGGCCGATCGT CCTCCTCCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4908 2.6e-09 45_[+2]_434 8643 1.8e-08 251_[+2]_228 264058 3.5e-08 391_[+2]_88 12172 9.9e-08 469_[+2]_10 18434 1.1e-07 427_[+2]_52 4338 1.9e-07 24_[+2]_455 261754 2.1e-07 435_[+2]_44 7978 2.8e-07 51_[+2]_428 33092 6.2e-07 61_[+2]_418 263089 8e-07 252_[+2]_227 11869 8.7e-07 162_[+2]_317 26536 1.1e-06 263_[+2]_216 4708 1.5e-06 435_[+2]_44 38726 1.6e-06 2_[+2]_477 11902 2e-06 417_[+2]_62 9491 2.2e-06 436_[+2]_43 4287 3.3e-06 4_[+2]_475 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=17 4908 ( 46) CCACCTCCACCGACAGTCACT 1 8643 ( 252) CCACCAAAACCGTCCAGCACT 1 264058 ( 392) CCACCACGAGCAACGAGCACA 1 12172 ( 470) ACACCAACAACGACGGACACA 1 18434 ( 428) ACACACCCAGCGGCAGCCACT 1 4338 ( 25) CCACCACCACCATCCCTACCA 1 261754 ( 436) CCACCACAGACGTCGAACAGT 1 7978 ( 52) TCAACGCCACCGGCAGGAACT 1 33092 ( 62) TCACGACCCACAACAAATCCT 1 263089 ( 253) TCAAGCCGAACAACGCCACCT 1 11869 ( 163) TCACGTCCAACAACTCCACCT 1 26536 ( 264) CCCAGCCCAACGACTAGCTCC 1 4708 ( 436) GCAAACCAAACAAGCAACACT 1 38726 ( 3) ACAAACTAAACAACAAGCACA 1 11902 ( 418) CCAACACCGCCCTCCATCTCT 1 9491 ( 437) CAAAGCCAAGCGGCACACACC 1 4287 ( 5) CCCCGACAACCGGCCGATCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 10.7007 E= 1.2e-002 -57 118 -202 -18 -215 201 -1073 -1073 176 -98 -1073 -1073 66 134 -1073 -1073 -57 101 56 -1073 85 60 -202 -118 -115 182 -1073 -218 43 118 -102 -1073 166 -198 -102 -1073 85 60 -44 -1073 -1073 210 -1073 -1073 66 -198 115 -1073 102 -1073 -2 -18 -1073 201 -202 -1073 43 34 -2 -118 85 1 30 -1073 43 -40 30 -60 -15 147 -1073 -118 117 34 -1073 -118 -1073 192 -102 -1073 -15 -98 -1073 128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 1.2e-002 0.176471 0.529412 0.058824 0.235294 0.058824 0.941176 0.000000 0.000000 0.882353 0.117647 0.000000 0.000000 0.411765 0.588235 0.000000 0.000000 0.176471 0.470588 0.352941 0.000000 0.470588 0.352941 0.058824 0.117647 0.117647 0.823529 0.000000 0.058824 0.352941 0.529412 0.117647 0.000000 0.823529 0.058824 0.117647 0.000000 0.470588 0.352941 0.176471 0.000000 0.000000 1.000000 0.000000 0.000000 0.411765 0.058824 0.529412 0.000000 0.529412 0.000000 0.235294 0.235294 0.000000 0.941176 0.058824 0.000000 0.352941 0.294118 0.235294 0.117647 0.470588 0.235294 0.294118 0.000000 0.352941 0.176471 0.294118 0.176471 0.235294 0.647059 0.000000 0.117647 0.588235 0.294118 0.000000 0.117647 0.000000 0.882353 0.117647 0.000000 0.235294 0.117647 0.000000 0.647059 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]CA[CA][CG][AC]C[CA]A[AC]C[GA][AGT]C[ACG][AGC][AG][CA][AC]C[TA] -------------------------------------------------------------------------------- Time 19.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 13 llr = 147 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :5::7::3:::3 pos.-specific C 6::9::9::::5 probability G 23112:17::a1 matrix T 229:1a::aa:1 bits 2.1 * 1.9 * *** 1.7 * ** *** 1.5 ** ** *** Relative 1.3 ** ** *** Entropy 1.1 ** ****** (16.3 bits) 0.8 ********* 0.6 * ********* 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CATCATCGTTGC consensus GG G A A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 269100 391 5.83e-08 TGAATCGCTG CATCATCGTTGC CAGAGCTACT 11869 249 5.83e-08 GCAGCGATTC CATCATCGTTGC TACTTTCTCC 23952 163 4.73e-07 TATTGTGTAG GATCATCGTTGC GGTAAAAGCG 37942 422 9.05e-07 CTGTGACACA CATCATCATTGA CTGACCGACG 22258 130 1.21e-06 TCTTGTGCGT TGTCATCGTTGC CACCGCCCTT 10381 132 1.69e-06 GATGAGAAGA GGTCATCGTTGA TGAAGGCTGA 264058 38 3.87e-06 TACTACTCGC CTTCTTCGTTGC ACCCCACCTC 264725 448 5.76e-06 ACACGCTTCA CAGCATCATTGC ATTGCTGGAA 9491 21 7.18e-06 TCAACATCAT CTTCATCATTGG CAAACTTGTA 4908 307 8.73e-06 CGTGATCGTC CGTCGTGGTTGC AGAAAAGCAA 4338 218 9.18e-06 AGGGTGGCGA TTTCGTCGTTGA GGGTTTCTAA 11966 237 9.70e-06 AGCACCTGTT CATCGTCATTGT TTCCTCAATG 7978 322 1.41e-05 GTGACTTGGT GGTGATCGTTGA TCCGTTGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269100 5.8e-08 390_[+3]_98 11869 5.8e-08 248_[+3]_240 23952 4.7e-07 162_[+3]_326 37942 9.1e-07 421_[+3]_67 22258 1.2e-06 129_[+3]_359 10381 1.7e-06 131_[+3]_357 264058 3.9e-06 37_[+3]_451 264725 5.8e-06 447_[+3]_41 9491 7.2e-06 20_[+3]_468 4908 8.7e-06 306_[+3]_182 4338 9.2e-06 217_[+3]_271 11966 9.7e-06 236_[+3]_252 7978 1.4e-05 321_[+3]_167 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=13 269100 ( 391) CATCATCGTTGC 1 11869 ( 249) CATCATCGTTGC 1 23952 ( 163) GATCATCGTTGC 1 37942 ( 422) CATCATCATTGA 1 22258 ( 130) TGTCATCGTTGC 1 10381 ( 132) GGTCATCGTTGA 1 264058 ( 38) CTTCTTCGTTGC 1 264725 ( 448) CAGCATCATTGC 1 9491 ( 21) CTTCATCATTGG 1 4908 ( 307) CGTCGTGGTTGC 1 4338 ( 218) TTTCGTCGTTGA 1 11966 ( 237) CATCGTCATTGT 1 7978 ( 322) GGTGATCGTTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16626 bayes= 10.8504 E= 3.5e+000 -1035 140 -5 -79 82 -1035 36 -21 -1035 -1035 -163 179 -1035 199 -163 -1035 141 -1035 -5 -179 -1035 -1035 -1035 191 -1035 199 -163 -1035 24 -1035 153 -1035 -1035 -1035 -1035 191 -1035 -1035 -1035 191 -1035 -1035 206 -1035 24 121 -163 -179 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 3.5e+000 0.000000 0.615385 0.230769 0.153846 0.461538 0.000000 0.307692 0.230769 0.000000 0.000000 0.076923 0.923077 0.000000 0.923077 0.076923 0.000000 0.692308 0.000000 0.230769 0.076923 0.000000 0.000000 0.000000 1.000000 0.000000 0.923077 0.076923 0.000000 0.307692 0.000000 0.692308 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.307692 0.538462 0.076923 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][AGT]TC[AG]TC[GA]TTG[CA] -------------------------------------------------------------------------------- Time 28.66 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10381 3.88e-04 131_[+3(1.69e-06)]_36_\ [+1(1.35e-05)]_89_[+1(7.41e-05)]_14_[+1(7.41e-05)]_155 11869 5.36e-08 67_[+1(3.45e-05)]_74_[+2(8.73e-07)]_\ 65_[+3(5.83e-08)]_240 11902 2.03e-04 174_[+1(7.70e-06)]_222_\ [+2(2.04e-06)]_62 11966 3.23e-03 236_[+3(9.70e-06)]_171_\ [+1(5.51e-05)]_60 12172 3.61e-04 469_[+2(9.88e-08)]_10 18434 7.50e-05 427_[+2(1.10e-07)]_52 22258 7.27e-05 129_[+3(1.21e-06)]_57_\ [+1(8.48e-06)]_281 22916 8.05e-04 301_[+1(2.93e-05)]_33_\ [+1(2.43e-07)]_124 2314 1.34e-03 249_[+1(3.82e-06)]_36_\ [+3(5.99e-05)]_182 23952 6.47e-06 45_[+1(6.12e-07)]_96_[+3(4.73e-07)]_\ 326 2495 3.55e-02 294_[+1(1.76e-05)]_185 261754 6.01e-07 8_[+3(7.74e-05)]_320_[+1(2.48e-05)]_\ 74_[+2(2.05e-07)]_9_[+1(1.60e-06)]_14 262764 2.82e-03 453_[+1(2.00e-06)]_26 263089 4.76e-05 252_[+2(8.04e-07)]_156_\ [+1(2.23e-06)]_50 264058 6.15e-10 37_[+3(3.87e-06)]_123_\ [+1(1.02e-07)]_90_[+3(7.38e-05)]_96_[+2(3.47e-08)]_88 264725 7.08e-05 210_[+1(2.49e-06)]_216_\ [+3(5.76e-06)]_41 26536 7.81e-04 53_[+1(6.89e-05)]_189_\ [+2(1.11e-06)]_216 269100 2.47e-05 255_[+1(1.76e-05)]_114_\ [+3(5.83e-08)]_98 33092 8.90e-07 61_[+2(6.24e-07)]_120_\ [+1(7.84e-07)]_277 3751 1.29e-01 191_[+1(7.41e-05)]_288 37942 1.40e-05 63_[+1(5.39e-07)]_337_\ [+3(9.05e-07)]_67 38726 8.75e-08 2_[+2(1.63e-06)]_206_[+1(1.12e-09)]_\ 250 41637 2.66e-01 354_[+1(7.41e-05)]_125 4287 3.16e-06 4_[+2(3.31e-06)]_419_[+1(1.59e-07)]_\ 35 4338 1.63e-08 24_[+2(1.86e-07)]_172_\ [+3(9.18e-06)]_40_[+1(6.40e-05)]_10_[+1(2.79e-07)]_179 4708 1.07e-03 352_[+1(5.94e-05)]_62_\ [+2(1.52e-06)]_44 4908 6.89e-10 45_[+2(2.57e-09)]_240_\ [+3(8.73e-06)]_97_[+1(6.93e-07)]_64 5010 1.41e-02 304_[+1(2.93e-05)]_175 5858 4.31e-03 222_[+1(2.78e-06)]_257 6541 8.40e-03 29_[+1(4.69e-06)]_32_[+1(5.11e-05)]_\ 397 7978 7.67e-06 51_[+2(2.75e-07)]_249_\ [+3(1.41e-05)]_167 8576 1.79e-01 500 8643 7.44e-07 149_[+1(9.32e-06)]_81_\ [+2(1.82e-08)]_228 9491 4.91e-07 20_[+3(7.18e-06)]_7_[+1(1.27e-06)]_\ 58_[+1(2.93e-05)]_297_[+2(2.19e-06)]_43 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************