******************************************************************************** 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/168/168.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11523 1.0000 500 11588 1.0000 500 1822 1.0000 500 20875 1.0000 500 21186 1.0000 500 22257 1.0000 500 22837 1.0000 500 23226 1.0000 500 23304 1.0000 500 23491 1.0000 500 23907 1.0000 500 24352 1.0000 500 24431 1.0000 500 25240 1.0000 500 260819 1.0000 500 34237 1.0000 500 35932 1.0000 500 4282 1.0000 500 5287 1.0000 500 5590 1.0000 500 6562 1.0000 500 6663 1.0000 500 8561 1.0000 500 8967 1.0000 500 9189 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/168/168.seqs.fa -oc motifs/168 -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= 25 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= 12500 N= 25 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.241 G 0.238 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.241 G 0.238 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 14 llr = 201 E-value = 7.6e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :2:7:534382194:45:6:1 pos.-specific C ::2:1:1::::1::1:1::3: probability G 238295346188:6941a449 matrix T 85:1::3211::11:14::31 bits 2.1 * 1.9 * 1.7 * * * 1.4 * * * Relative 1.2 * * * * * * * * Entropy 1.0 * * ** **** * ** * (20.7 bits) 0.8 * **** ****** ** * 0.6 * **** ******** ** * 0.4 ****** ************** 0.2 ****** ************** 0.0 --------------------- Multilevel TTGAGAAAGAGGAGGAAGAGG consensus GGCG GGGA A A GT GC sequence A TT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 34237 35 9.27e-10 TGAGGAAGGG TTGAGGTTGAGGAGGTTGAGG AGGAGACTTC 22837 238 1.08e-09 TTCAACAGTG TTGAGACAAAGGAAGGAGAGG AATCTCTTTA 35932 95 1.35e-08 GGAGGCTGTG TAGAGGAGGAGGAGGAGGGCG GAGAGGAGGG 9189 114 1.51e-08 GAAGGTGGAG GTGAGAAAGGGGAGGAAGGTG GATGTAACAT 8967 140 2.10e-08 GGCGTGATGA TGGAGAAAAAAGAAGGTGATG GACGGCGGCG 11588 190 6.35e-08 TTTCGGATGG TTCAGAGGTAGAAGGGAGGGG CCGACGCTTA 5590 121 1.54e-07 CTCATTGTGT TGGAGAGTTTGGAAGGAGGGG ACAGCGAGCT 25240 9 1.54e-07 TGCCCATC TTGGGGAAGGAGAGGTTGATG AATGGTTTTG 23226 150 1.97e-07 GAGGAAGAGC TTGTCATGGAGGAGGGTGGTG TAGGCGCTAC 21186 54 2.50e-07 CATCGGCTGG TACAGGTAAAGCAAGAAGACG AACTATATCT 6663 380 3.65e-07 TTTGGATGTA GTGGGAGGGAAGAAGAAGAGT TGAAGAGGGA 4282 63 4.22e-07 GCATGTTTGG TGGGGGCGGAGGTGGAAGACA AGCTGTGCCA 6562 52 5.59e-07 GAACCGAGGA GAGAGGTTGAGGTTGATGACG ATCGTAGCAC 11523 98 1.45e-06 AGCGAGTCCA TGCAGGGAAAGAAGCGCGAGG ACGAACCCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34237 9.3e-10 34_[+1]_445 22837 1.1e-09 237_[+1]_242 35932 1.3e-08 94_[+1]_385 9189 1.5e-08 113_[+1]_366 8967 2.1e-08 139_[+1]_340 11588 6.4e-08 189_[+1]_290 5590 1.5e-07 120_[+1]_359 25240 1.5e-07 8_[+1]_471 23226 2e-07 149_[+1]_330 21186 2.5e-07 53_[+1]_426 6663 3.6e-07 379_[+1]_100 4282 4.2e-07 62_[+1]_417 6562 5.6e-07 51_[+1]_428 11523 1.4e-06 97_[+1]_382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=14 34237 ( 35) TTGAGGTTGAGGAGGTTGAGG 1 22837 ( 238) TTGAGACAAAGGAAGGAGAGG 1 35932 ( 95) TAGAGGAGGAGGAGGAGGGCG 1 9189 ( 114) GTGAGAAAGGGGAGGAAGGTG 1 8967 ( 140) TGGAGAAAAAAGAAGGTGATG 1 11588 ( 190) TTCAGAGGTAGAAGGGAGGGG 1 5590 ( 121) TGGAGAGTTTGGAAGGAGGGG 1 25240 ( 9) TTGGGGAAGGAGAGGTTGATG 1 23226 ( 150) TTGTCATGGAGGAGGGTGGTG 1 21186 ( 54) TACAGGTAAAGCAAGAAGACG 1 6663 ( 380) GTGGGAGGGAAGAAGAAGAGT 1 4282 ( 63) TGGGGGCGGAGGTGGAAGACA 1 6562 ( 52) GAGAGGTTGAGGTTGATGACG 1 11523 ( 98) TGCAGGGAAAGAAGCGCGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 10.348 E= 7.6e-007 -1045 -1045 -15 161 -30 -1045 26 96 -1045 -17 172 -1045 143 -1045 -15 -184 -1045 -175 196 -1045 92 -1045 107 -1045 11 -75 26 15 70 -1045 58 -26 11 -1045 126 -84 157 -1045 -74 -184 -30 -1045 172 -1045 -89 -175 172 -1045 170 -1045 -1045 -84 44 -1045 126 -184 -1045 -175 196 -1045 70 -1045 85 -84 92 -175 -173 48 -1045 -1045 207 -1045 128 -1045 58 -1045 -1045 24 85 15 -188 -1045 185 -184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 14 E= 7.6e-007 0.000000 0.000000 0.214286 0.785714 0.214286 0.000000 0.285714 0.500000 0.000000 0.214286 0.785714 0.000000 0.714286 0.000000 0.214286 0.071429 0.000000 0.071429 0.928571 0.000000 0.500000 0.000000 0.500000 0.000000 0.285714 0.142857 0.285714 0.285714 0.428571 0.000000 0.357143 0.214286 0.285714 0.000000 0.571429 0.142857 0.785714 0.000000 0.142857 0.071429 0.214286 0.000000 0.785714 0.000000 0.142857 0.071429 0.785714 0.000000 0.857143 0.000000 0.000000 0.142857 0.357143 0.000000 0.571429 0.071429 0.000000 0.071429 0.928571 0.000000 0.428571 0.000000 0.428571 0.142857 0.500000 0.071429 0.071429 0.357143 0.000000 0.000000 1.000000 0.000000 0.642857 0.000000 0.357143 0.000000 0.000000 0.285714 0.428571 0.285714 0.071429 0.000000 0.857143 0.071429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][TGA][GC][AG]G[AG][AGT][AGT][GA]A[GA]GA[GA]G[AG][AT]G[AG][GCT]G -------------------------------------------------------------------------------- Time 6.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 23 llr = 257 E-value = 2.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::1::2:1::11::3:3:: pos.-specific C 21:::1:::11113::::2 probability G :75:87472571156:336 matrix T 82492:6274:7821a362 bits 2.1 1.9 1.7 * 1.4 ** * Relative 1.2 * ** * Entropy 1.0 * ** * * (16.1 bits) 0.8 ** ** * * * * ** 0.6 **************** ** 0.4 **************** ** 0.2 ******************* 0.0 ------------------- Multilevel TGGTGGTGTGGTTGGTTTG consensus C T GT T CA AGC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 25240 362 1.30e-09 AACAAGTTTG TGGTGGTGTGGCTGGTTTG GGAGACTCTC 8967 85 4.16e-08 ACGAGAGTCA TGGTGATGTTGTTGATTGT AGAGTGTGGC 35932 127 4.74e-08 AGAGGAGGGT TATTGGTGTTGTTGGTAGG CGTGCCATGG 11588 224 2.54e-07 ACGCTTACGT CGGTGGGATTGTTCATATG TCATGGACCT 9189 62 4.39e-07 GGTTCGGTAC TGGTGGCGTGGAGGGTGTG TGGCGGTGGC 22257 166 4.88e-07 TATTGGTCGG TGTTGGTGGCGTTGGTTCG CCGCTTGTCT 11523 197 4.88e-07 CCGCGGAGTA TGGTGGGTGGATTCATTTG TATAGTAGTA 20875 163 5.42e-07 GTGTGTGTCG TCATGGTGTTATTGGTGTG AGGCAACCAC 6562 83 9.99e-07 ATCGTAGCAC CGGTGATGATGTTGATGTG AGCGATCGCT 23491 167 2.82e-06 GCAAGATTCA TGGTGAGGGCGATGGTATC TTTTTTTACA 23907 225 3.08e-06 TACCTCTGAG TGTTGGTGTTGTCTATCTC GTATCGAGTT 22837 123 3.08e-06 AAGGATCCGG CGGGGGGATGGTTGGTGTC AACTCTTTGA 5287 261 3.37e-06 GGGTCTGGTC TGTTGCTGCTGTGCGTTGG AGGCGTATGA 21186 321 5.19e-06 GGACATAGAA TTGTGGGGGGGGTCATAGT GAACCAGTTA 24352 60 5.65e-06 ATCTTCCCAT TTGTGGTTTGCCTCGTTTT GGTGGTCGTT 5590 152 6.67e-06 ACAGCGAGCT TGGTTGGGTGTTTGTTGGC GACTATCACT 23226 190 7.25e-06 CATTCGACTT CGTTTGTGTGGGCTGTTTG CTGATTGCTC 24431 252 8.52e-06 GAGTGTGAGT TGATGTGTTTGTGGGTGGG TGATGAAGAA 1822 250 8.52e-06 CTGCCGTGAC TTTTGATGTGATTCTTATT GCTGTTCTCT 4282 35 9.23e-06 AGGAATGGAA TGTTTGGTTGGATGGGAGG CATGTTTGGT 34237 442 1.26e-05 TTAGATCGAT CGTTGCTTTGGTTTGTTAT CAAAGTGTTT 8561 289 1.71e-05 GGATGAGCAC TCTCTGGGTTGTTTATATG ATTGTTAAAG 6663 241 1.99e-05 TGAGGTGGAG TTGTGCTCTTCTTCGTGTC GGAGCTGCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25240 1.3e-09 361_[+2]_120 8967 4.2e-08 84_[+2]_397 35932 4.7e-08 126_[+2]_355 11588 2.5e-07 223_[+2]_258 9189 4.4e-07 61_[+2]_420 22257 4.9e-07 165_[+2]_316 11523 4.9e-07 196_[+2]_285 20875 5.4e-07 162_[+2]_319 6562 1e-06 82_[+2]_399 23491 2.8e-06 166_[+2]_315 23907 3.1e-06 224_[+2]_257 22837 3.1e-06 122_[+2]_359 5287 3.4e-06 260_[+2]_221 21186 5.2e-06 320_[+2]_161 24352 5.6e-06 59_[+2]_422 5590 6.7e-06 151_[+2]_330 23226 7.2e-06 189_[+2]_292 24431 8.5e-06 251_[+2]_230 1822 8.5e-06 249_[+2]_232 4282 9.2e-06 34_[+2]_447 34237 1.3e-05 441_[+2]_40 8561 1.7e-05 288_[+2]_193 6663 2e-05 240_[+2]_241 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=23 25240 ( 362) TGGTGGTGTGGCTGGTTTG 1 8967 ( 85) TGGTGATGTTGTTGATTGT 1 35932 ( 127) TATTGGTGTTGTTGGTAGG 1 11588 ( 224) CGGTGGGATTGTTCATATG 1 9189 ( 62) TGGTGGCGTGGAGGGTGTG 1 22257 ( 166) TGTTGGTGGCGTTGGTTCG 1 11523 ( 197) TGGTGGGTGGATTCATTTG 1 20875 ( 163) TCATGGTGTTATTGGTGTG 1 6562 ( 83) CGGTGATGATGTTGATGTG 1 23491 ( 167) TGGTGAGGGCGATGGTATC 1 23907 ( 225) TGTTGGTGTTGTCTATCTC 1 22837 ( 123) CGGGGGGATGGTTGGTGTC 1 5287 ( 261) TGTTGCTGCTGTGCGTTGG 1 21186 ( 321) TTGTGGGGGGGGTCATAGT 1 24352 ( 60) TTGTGGTTTGCCTCGTTTT 1 5590 ( 152) TGGTTGGGTGTTTGTTGGC 1 23226 ( 190) CGTTTGTGTGGGCTGTTTG 1 24431 ( 252) TGATGTGTTTGTGGGTGGG 1 1822 ( 250) TTTTGATGTGATTCTTATT 1 4282 ( 35) TGTTTGGTTGGATGGGAGG 1 34237 ( 442) CGTTGCTTTGGTTTGTTAT 1 8561 ( 289) TCTCTGGGTTGTTTATATG 1 6663 ( 241) TTGTGCTCTTCTTCGTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 12050 bayes= 10.096 E= 2.2e-008 -1117 -15 -1117 161 -260 -147 155 -56 -160 -1117 113 61 -1117 -247 -245 183 -1117 -1117 179 -56 -60 -89 145 -256 -1117 -247 72 114 -160 -247 145 -24 -260 -247 -45 153 -1117 -147 101 76 -102 -147 163 -256 -102 -147 -145 144 -1117 -147 -87 161 -1117 34 113 -56 20 -1117 135 -156 -1117 -1117 -245 190 20 -247 35 44 -260 -247 35 125 -1117 -15 125 -24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 23 E= 2.2e-008 0.000000 0.217391 0.000000 0.782609 0.043478 0.086957 0.695652 0.173913 0.086957 0.000000 0.521739 0.391304 0.000000 0.043478 0.043478 0.913043 0.000000 0.000000 0.826087 0.173913 0.173913 0.130435 0.652174 0.043478 0.000000 0.043478 0.391304 0.565217 0.086957 0.043478 0.652174 0.217391 0.043478 0.043478 0.173913 0.739130 0.000000 0.086957 0.478261 0.434783 0.130435 0.086957 0.739130 0.043478 0.130435 0.086957 0.086957 0.695652 0.000000 0.086957 0.130435 0.782609 0.000000 0.304348 0.521739 0.173913 0.304348 0.000000 0.608696 0.086957 0.000000 0.000000 0.043478 0.956522 0.304348 0.043478 0.304348 0.347826 0.043478 0.043478 0.304348 0.608696 0.000000 0.217391 0.565217 0.217391 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC]G[GT]TGG[TG][GT]T[GT]GTT[GC][GA]T[TAG][TG][GCT] -------------------------------------------------------------------------------- Time 13.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 24 llr = 265 E-value = 2.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 12892515635167:86:861 pos.-specific C 562174644338118:262:9 probability G :2:::12::2211::2:2:2: matrix T 4:::111::3::121:2212: bits 2.1 1.9 1.7 1.4 * * Relative 1.2 * * * Entropy 1.0 ** ** * (15.9 bits) 0.8 *** ** * ** * * 0.6 ***** ** * ******** 0.4 ********* *********** 0.2 ********* *********** 0.0 --------------------- Multilevel CCAACACAACACAACAACAAC consensus TA AC CCTC GTT G sequence AG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6562 451 4.05e-08 ACTGCAACCC TCCACCCACCACGACAAGAAC TTGACGACCA 25240 472 4.05e-08 AAGCCAAGGT TGAACATCACACGACAACAAC ATGAGACC 24352 287 4.61e-08 CCTCTATTCA TCAATACAATACAACATTAAC CTTGGCAGTG 20875 370 8.64e-08 CAAATTCTGC TCAACAACCTACAACAACAAA CCACCGTCGA 11523 480 9.76e-08 CTCATAAATC TCAAACCACAACACCATCAAC 5287 443 1.58e-07 CTTTGCTGCT CCAACACCCTCCAACGATCGC GTGCAGACTG 23226 322 2.00e-07 CAGCCAGCCC CCAACACCACACCATAACCTC GTCGAAGACT 34237 236 4.37e-07 ATCAATCTTT TCAAACTCACACAAAAACAAC TCAAAACAAA 21186 435 5.41e-07 AGTCTTCTCT CAAACTCACTCCTTCAACAAC TGCTTCGGCA 9189 304 6.01e-07 ACACAAGCAC CCAACCAACGCCAACGCCAGC AGCCACAGTC 23907 305 6.01e-07 CTGGTGATTG TGACCGCCCCACATCAACAAC CACTTCTTGA 5590 263 1.50e-06 CAAACCAAGC TCGCCTCAAAGCAACAACAAC GAAGCGTGTA 35932 480 4.14e-06 ATCTCATCAA CAACAACAAACCATCATCATC 11588 477 4.93e-06 TAACTTCCTG ACAACATCAAAACACATCATC AAA 23304 392 5.37e-06 CTCTCAAACT TCAACCCACTGCAATACGAAT CTGTTGGTGC 8967 434 6.93e-06 TGCCCTTCAT CACACACATCACAGCGACAAC CGTCACCAAT 260819 18 8.88e-06 GCTGGAACTA TCAACCCAAGAGAATATTCGC CTATCCACAC 22257 466 1.13e-05 AGTATAATCT CCCACACCAGCTAAGAAGAAC TCATAATCCA 23491 330 1.94e-05 AGCAGATTCG CCAAAAGCAAAGGACAAGCTC CACTACTGAA 6663 69 2.09e-05 GGATAAAGCC CGAACAGAATCAAACGATTGC TTTGCAAGGG 4282 130 2.43e-05 ATAGGAGATT AGAAACGAACCATTCAACAAC AAACTAAGAG 8561 460 2.80e-05 GCTACTACTG CCAACGCACAGCACCACTAGA CACCACATAC 1822 110 3.72e-05 CTGTCATTTG CAAACCCGAGGCCACGCCTAC ACTGCTACCT 22837 278 3.98e-05 ACGCAACACA AACATCGCATGCTACAACATC CTAGTTCTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6562 4e-08 450_[+3]_29 25240 4e-08 471_[+3]_8 24352 4.6e-08 286_[+3]_193 20875 8.6e-08 369_[+3]_110 11523 9.8e-08 479_[+3] 5287 1.6e-07 442_[+3]_37 23226 2e-07 321_[+3]_158 34237 4.4e-07 235_[+3]_244 21186 5.4e-07 434_[+3]_45 9189 6e-07 303_[+3]_176 23907 6e-07 304_[+3]_175 5590 1.5e-06 262_[+3]_217 35932 4.1e-06 479_[+3] 11588 4.9e-06 476_[+3]_3 23304 5.4e-06 391_[+3]_88 8967 6.9e-06 433_[+3]_46 260819 8.9e-06 17_[+3]_462 22257 1.1e-05 465_[+3]_14 23491 1.9e-05 329_[+3]_150 6663 2.1e-05 68_[+3]_411 4282 2.4e-05 129_[+3]_350 8561 2.8e-05 459_[+3]_20 1822 3.7e-05 109_[+3]_370 22837 4e-05 277_[+3]_202 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=24 6562 ( 451) TCCACCCACCACGACAAGAAC 1 25240 ( 472) TGAACATCACACGACAACAAC 1 24352 ( 287) TCAATACAATACAACATTAAC 1 20875 ( 370) TCAACAACCTACAACAACAAA 1 11523 ( 480) TCAAACCACAACACCATCAAC 1 5287 ( 443) CCAACACCCTCCAACGATCGC 1 23226 ( 322) CCAACACCACACCATAACCTC 1 34237 ( 236) TCAAACTCACACAAAAACAAC 1 21186 ( 435) CAAACTCACTCCTTCAACAAC 1 9189 ( 304) CCAACCAACGCCAACGCCAGC 1 23907 ( 305) TGACCGCCCCACATCAACAAC 1 5590 ( 263) TCGCCTCAAAGCAACAACAAC 1 35932 ( 480) CAACAACAAACCATCATCATC 1 11588 ( 477) ACAACATCAAAACACATCATC 1 23304 ( 392) TCAACCCACTGCAATACGAAT 1 8967 ( 434) CACACACATCACAGCGACAAC 1 260819 ( 18) TCAACCCAAGAGAATATTCGC 1 22257 ( 466) CCCACACCAGCTAAGAAGAAC 1 23491 ( 330) CCAAAAGCAAAGGACAAGCTC 1 6663 ( 69) CGAACAGAATCAAACGATTGC 1 4282 ( 130) AGAAACGAACCATTCAACAAC 1 8561 ( 460) CCAACGCACAGCACCACTAGA 1 1822 ( 110) CAAACCCGAGGCCACGCCTAC 1 22837 ( 278) AACATCGCATGCTACAACATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 9.41113 E= 2.8e-006 -108 93 -1123 70 -34 137 -51 -1123 158 -53 -251 -1123 173 -95 -1123 -1123 -34 155 -1123 -162 80 64 -151 -162 -166 137 -51 -104 104 79 -251 -1123 114 64 -1123 -262 -8 27 -51 18 92 27 -19 -1123 -108 164 -151 -262 124 -95 -93 -104 142 -153 -251 -62 -266 171 -251 -104 158 -1123 -19 -1123 124 -53 -1123 -30 -1123 137 -51 -30 151 -53 -1123 -162 114 -1123 -19 -30 -166 186 -1123 -262 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 2.8e-006 0.125000 0.458333 0.000000 0.416667 0.208333 0.625000 0.166667 0.000000 0.791667 0.166667 0.041667 0.000000 0.875000 0.125000 0.000000 0.000000 0.208333 0.708333 0.000000 0.083333 0.458333 0.375000 0.083333 0.083333 0.083333 0.625000 0.166667 0.125000 0.541667 0.416667 0.041667 0.000000 0.583333 0.375000 0.000000 0.041667 0.250000 0.291667 0.166667 0.291667 0.500000 0.291667 0.208333 0.000000 0.125000 0.750000 0.083333 0.041667 0.625000 0.125000 0.125000 0.125000 0.708333 0.083333 0.041667 0.166667 0.041667 0.791667 0.041667 0.125000 0.791667 0.000000 0.208333 0.000000 0.625000 0.166667 0.000000 0.208333 0.000000 0.625000 0.166667 0.208333 0.750000 0.166667 0.000000 0.083333 0.583333 0.000000 0.208333 0.208333 0.083333 0.875000 0.000000 0.041667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CA]AA[CA][AC]C[AC][AC][CTA][ACG]CAAC[AG][AT][CT]A[AGT]C -------------------------------------------------------------------------------- Time 19.97 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11523 2.71e-09 97_[+1(1.45e-06)]_78_[+2(4.88e-07)]_\ 264_[+3(9.76e-08)] 11588 3.09e-09 189_[+1(6.35e-08)]_13_\ [+2(2.54e-07)]_234_[+3(4.93e-06)]_3 1822 4.06e-03 109_[+3(3.72e-05)]_119_\ [+2(8.52e-06)]_232 20875 6.68e-07 95_[+2(7.20e-05)]_48_[+2(5.42e-07)]_\ 188_[+3(8.64e-08)]_29_[+3(7.70e-05)]_36_[+3(4.88e-05)]_3 21186 2.30e-08 53_[+1(2.50e-07)]_197_\ [+1(7.43e-05)]_28_[+2(5.19e-06)]_95_[+3(5.41e-07)]_45 22257 7.55e-05 117_[+2(6.35e-05)]_29_\ [+2(4.88e-07)]_281_[+3(1.13e-05)]_14 22837 4.92e-09 122_[+2(3.08e-06)]_96_\ [+1(1.08e-09)]_19_[+3(3.98e-05)]_202 23226 1.00e-08 149_[+1(1.97e-07)]_19_\ [+2(7.25e-06)]_113_[+3(2.00e-07)]_158 23304 4.38e-03 391_[+3(5.37e-06)]_88 23491 4.83e-04 166_[+2(2.82e-06)]_144_\ [+3(1.94e-05)]_150 23907 1.75e-05 147_[+3(8.72e-05)]_56_\ [+2(3.08e-06)]_61_[+3(6.01e-07)]_175 24352 2.04e-06 59_[+2(5.65e-06)]_163_\ [+3(4.88e-05)]_24_[+3(4.61e-08)]_193 24431 4.35e-02 251_[+2(8.52e-06)]_230 25240 5.70e-13 8_[+1(1.54e-07)]_332_[+2(1.30e-09)]_\ 30_[+1(2.99e-05)]_40_[+3(4.05e-08)]_8 260819 5.69e-02 17_[+3(8.88e-06)]_462 34237 2.42e-10 34_[+1(9.27e-10)]_180_\ [+3(4.37e-07)]_185_[+2(1.26e-05)]_40 35932 1.31e-10 94_[+1(1.35e-08)]_11_[+2(4.74e-08)]_\ 25_[+1(7.93e-05)]_288_[+3(4.14e-06)] 4282 1.96e-06 34_[+2(9.23e-06)]_9_[+1(4.22e-07)]_\ 46_[+3(2.43e-05)]_350 5287 7.36e-06 260_[+2(3.37e-06)]_163_\ [+3(1.58e-07)]_37 5590 4.71e-08 65_[+1(9.02e-05)]_34_[+1(1.54e-07)]_\ 10_[+2(6.67e-06)]_92_[+3(1.50e-06)]_217 6562 9.64e-10 51_[+1(5.59e-07)]_10_[+2(9.99e-07)]_\ 349_[+3(4.05e-08)]_29 6663 2.99e-06 68_[+3(2.09e-05)]_151_\ [+2(1.99e-05)]_120_[+1(3.65e-07)]_100 8561 3.61e-03 288_[+2(1.71e-05)]_152_\ [+3(2.80e-05)]_20 8967 2.83e-10 84_[+2(4.16e-08)]_36_[+1(2.10e-08)]_\ 273_[+3(6.93e-06)]_46 9189 1.92e-10 61_[+2(4.39e-07)]_33_[+1(1.51e-08)]_\ 169_[+3(6.01e-07)]_176 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************