******************************************************************************** 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/429/429.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10025 1.0000 500 10189 1.0000 500 10558 1.0000 500 10559 1.0000 500 10788 1.0000 500 1880 1.0000 500 20945 1.0000 500 21599 1.0000 500 22596 1.0000 500 23050 1.0000 500 23791 1.0000 500 23806 1.0000 500 24888 1.0000 500 25141 1.0000 500 25182 1.0000 500 263031 1.0000 500 269935 1.0000 500 3021 1.0000 500 3098 1.0000 500 34293 1.0000 500 34672 1.0000 500 40627 1.0000 500 6483 1.0000 500 9203 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/429/429.seqs.fa -oc motifs/429 -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= 24 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= 12000 N= 24 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.251 C 0.242 G 0.237 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.251 C 0.242 G 0.237 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 24 llr = 244 E-value = 3.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5813452a:6742893 pos.-specific C 3376218:94:58317 probability G 2:1131::::1:1::: matrix T ::::231:::22:::: bits 2.1 * 1.9 * 1.7 * * 1.5 * * Relative 1.2 * ** ** Entropy 1.0 * *** *** (14.7 bits) 0.8 *** **** **** 0.6 **** ********** 0.4 **** ********** 0.2 **** *********** 0.0 ---------------- Multilevel AACCAACACAACCAAC consensus CC AGT CTA C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 22596 485 4.37e-08 ACACAAGCAC AACCCGCACAACCAAC 9203 377 8.51e-08 CTTCTCCAAC AACCACCACCAACAAC CCTCTACGCC 10025 484 8.51e-08 TTGAGACCTC CCCCAACACCAACAAC A 3098 386 2.05e-07 ACAAGGAGAC AAACCACACAAACAAC CCTGTTCAAA 40627 464 2.77e-07 CAACACAACC GACCGACACAACAAAC CACACACACA 10189 277 9.81e-07 CAACGCAAGT AACCTCCACCTCCAAC CAGCCCTCGC 3021 307 1.10e-06 CTTGGTGGCA ACCAATAACAAACAAC GTTGTTGTGG 10559 469 2.40e-06 TCGAATATAT CACCATCACATAGAAC CGATAACCAC 21599 242 2.96e-06 GTAGGTGGCA AAGGAACACAAACAAA GTGAGTACTT 1880 467 4.00e-06 GCCCATCTTG ACCCTTCACCTACCAC AAGCTCACAT 6483 472 5.37e-06 CTTCTCTAGC GACACAAACATCCAAC CCTCGAATCT 25141 149 6.47e-06 TTTTCTGCCT GCCCGTCACAACACAC GGGCCTCTCG 34672 131 7.11e-06 TCATCCGAGT CATATTCACCACCAAC ACTGCCTCTA 20945 422 7.11e-06 TTTAAGATTG AACACGCACAATCCAA GCTTTAAAAA 263031 463 9.30e-06 CCTTCAAACC AACCAACACCGACACA CCGCCAAAAT 23806 348 1.11e-05 GGTACTTCAC AACAGGCACACCCCAC CCTAGCTTCT 23791 308 1.11e-05 CGACGGCAAG ACAAGTCACCAACCAC AGACGTCATC 10788 427 1.69e-05 GCCCACCCAA CAACAATACAACCCAA CGTCTCTCAG 24888 158 3.65e-05 GCTGTCTACG AAGCTACACCTTCACC TGCCGGCTCA 34293 263 3.92e-05 CTCTACGCTG CAGCTTCATAATCAAC GGCAATTTCT 25182 485 4.52e-05 TCTCTGCTCA ACCCGATACAGTCAAA 269935 400 9.35e-05 GGGTTAAAAA GACCATAAGCACAAAA AGAGACCTCA 23050 404 1.34e-04 GTCACTAATT CACAAACAAGACAAAA CAGATCCTGG 10558 162 1.59e-04 TTGGGGTGAT CACGGAAACAACGAAT TGCAAGTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22596 4.4e-08 484_[+1] 9203 8.5e-08 376_[+1]_108 10025 8.5e-08 483_[+1]_1 3098 2.1e-07 385_[+1]_99 40627 2.8e-07 463_[+1]_21 10189 9.8e-07 276_[+1]_208 3021 1.1e-06 306_[+1]_178 10559 2.4e-06 468_[+1]_16 21599 3e-06 241_[+1]_243 1880 4e-06 466_[+1]_18 6483 5.4e-06 471_[+1]_13 25141 6.5e-06 148_[+1]_336 34672 7.1e-06 130_[+1]_354 20945 7.1e-06 421_[+1]_63 263031 9.3e-06 462_[+1]_22 23806 1.1e-05 347_[+1]_137 23791 1.1e-05 307_[+1]_177 10788 1.7e-05 426_[+1]_58 24888 3.6e-05 157_[+1]_327 34293 3.9e-05 262_[+1]_222 25182 4.5e-05 484_[+1] 269935 9.4e-05 399_[+1]_85 23050 0.00013 403_[+1]_81 10558 0.00016 161_[+1]_323 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=24 22596 ( 485) AACCCGCACAACCAAC 1 9203 ( 377) AACCACCACCAACAAC 1 10025 ( 484) CCCCAACACCAACAAC 1 3098 ( 386) AAACCACACAAACAAC 1 40627 ( 464) GACCGACACAACAAAC 1 10189 ( 277) AACCTCCACCTCCAAC 1 3021 ( 307) ACCAATAACAAACAAC 1 10559 ( 469) CACCATCACATAGAAC 1 21599 ( 242) AAGGAACACAAACAAA 1 1880 ( 467) ACCCTTCACCTACCAC 1 6483 ( 472) GACACAAACATCCAAC 1 25141 ( 149) GCCCGTCACAACACAC 1 34672 ( 131) CATATTCACCACCAAC 1 20945 ( 422) AACACGCACAATCCAA 1 263031 ( 463) AACCAACACCGACACA 1 23806 ( 348) AACAGGCACACCCCAC 1 23791 ( 308) ACAAGTCACCAACCAC 1 10788 ( 427) CAACAATACAACCCAA 1 24888 ( 158) AAGCTACACCTTCACC 1 34293 ( 263) CAGCTTCATAATCAAC 1 25182 ( 485) ACCCGATACAGTCAAA 1 269935 ( 400) GACCATAAGCACAAAA 1 23050 ( 404) CACAAACAAGACAAAA 1 10558 ( 162) CACGGAAACAACGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11640 bayes= 8.91886 E= 3.3e-009 111 27 -51 -1123 158 5 -1123 -1123 -100 155 -92 -270 22 137 -151 -1123 58 -54 8 -38 87 -154 -92 30 -59 163 -1123 -170 200 -1123 -1123 -1123 -259 186 -250 -270 122 63 -250 -1123 141 -253 -151 -38 58 92 -1123 -70 -59 163 -151 -1123 158 5 -1123 -1123 187 -154 -1123 -1123 22 146 -1123 -270 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 3.3e-009 0.541667 0.291667 0.166667 0.000000 0.750000 0.250000 0.000000 0.000000 0.125000 0.708333 0.125000 0.041667 0.291667 0.625000 0.083333 0.000000 0.375000 0.166667 0.250000 0.208333 0.458333 0.083333 0.125000 0.333333 0.166667 0.750000 0.000000 0.083333 1.000000 0.000000 0.000000 0.000000 0.041667 0.875000 0.041667 0.041667 0.583333 0.375000 0.041667 0.000000 0.666667 0.041667 0.083333 0.208333 0.375000 0.458333 0.000000 0.166667 0.166667 0.750000 0.083333 0.000000 0.750000 0.250000 0.000000 0.000000 0.916667 0.083333 0.000000 0.000000 0.291667 0.666667 0.000000 0.041667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AC]C[CA][AGT][AT]CAC[AC][AT][CA]C[AC]A[CA] -------------------------------------------------------------------------------- Time 5.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 20 llr = 218 E-value = 3.9e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4:33114::4::::1 pos.-specific C 22::1:::::2::21: probability G 8:8526923a181192 matrix T :43353:581429817 bits 2.1 1.9 * 1.7 * * 1.5 * * * * Relative 1.2 * * * * ** * Entropy 1.0 * * * ** **** (15.7 bits) 0.8 * * * ** ***** 0.6 * * ** ** ***** 0.4 **** ***** ***** 0.2 **************** 0.0 ---------------- Multilevel GAGGTGGTTGAGTTGT consensus CTTTAT AG TT G sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 3098 150 3.86e-09 TCGTTTGTTG GAGATGGTTGAGTTGT GTGTTCTTTT 22596 241 1.24e-08 GAACTGAGCA GAGGTTGTTGTGTTGT CGTCAATCCG 9203 30 7.76e-08 GGTTAGGAGG GAGGAGGATGTGTTGG TTTTTCTGTG 21599 197 1.25e-07 ACGATGATTT GATGTTGATGAGTTGT TGTGATTGAT 269935 167 6.07e-07 GCTGAGCGTT GTGTAGGATGCGTTGG GGTGTTGCTG 25141 243 8.56e-07 CGGCTCGGAG GCGAAGGTTGTGTCGT ACACTCCACA 25182 125 2.92e-06 GGCACCCGAC CAGTTGGATGGGTTGG ATCCCTTTTT 23806 160 3.50e-06 ATATCTCGAG GTTGAGGATGAGTTTT AACTTTTCGC 23050 26 3.84e-06 GTTCGTTGAC GAGAGGATGGAGTTGT TTCGACTTTT 34293 100 4.99e-06 TGAGCGTGAT GATGGGGGTGAGTTGA TGTGATGGAC 10558 340 4.99e-06 TGTTTTAATG GTGTTGGTGGATGTGT GAAGAAGATG 10025 190 5.43e-06 GACGTAGAAA CTGATGGATGAGTTCT TGGAGTTCAT 3021 268 6.41e-06 CGTTCGAGCG GTTGTAGTGGTGTTGG AGGAATTGAC 263031 2 1.11e-05 C CTGGATGTTGATTTGA CTGCTGATTT 40627 145 1.20e-05 ATCGTGGGCT GCTGCTGGTGTGTTGT TGGCCTCCGC 10189 32 1.20e-05 GGTCTGTGGG GCGTGAGTGGCGTTGT TGCTAGCACC 10559 31 1.29e-05 GCTTCTGCGG CAGATGGAGGTGTGGT TGGTGCCGAG 34672 48 1.38e-05 TATCGTCCTC GTGGTTGTTGTTGCGT GATTTGGAGC 10788 287 2.90e-05 TCATCTTTTT GTGTTTGTTTGTTTGT TTGATATTTT 20945 121 3.28e-05 GCCGGTGGTC GCGTAGAGTGCGTCGT CTTCTACTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3098 3.9e-09 149_[+2]_335 22596 1.2e-08 240_[+2]_244 9203 7.8e-08 29_[+2]_455 21599 1.2e-07 196_[+2]_288 269935 6.1e-07 166_[+2]_318 25141 8.6e-07 242_[+2]_242 25182 2.9e-06 124_[+2]_360 23806 3.5e-06 159_[+2]_325 23050 3.8e-06 25_[+2]_459 34293 5e-06 99_[+2]_385 10558 5e-06 339_[+2]_145 10025 5.4e-06 189_[+2]_295 3021 6.4e-06 267_[+2]_217 263031 1.1e-05 1_[+2]_483 40627 1.2e-05 144_[+2]_340 10189 1.2e-05 31_[+2]_453 10559 1.3e-05 30_[+2]_454 34672 1.4e-05 47_[+2]_437 10788 2.9e-05 286_[+2]_198 20945 3.3e-05 120_[+2]_364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=20 3098 ( 150) GAGATGGTTGAGTTGT 1 22596 ( 241) GAGGTTGTTGTGTTGT 1 9203 ( 30) GAGGAGGATGTGTTGG 1 21599 ( 197) GATGTTGATGAGTTGT 1 269935 ( 167) GTGTAGGATGCGTTGG 1 25141 ( 243) GCGAAGGTTGTGTCGT 1 25182 ( 125) CAGTTGGATGGGTTGG 1 23806 ( 160) GTTGAGGATGAGTTTT 1 23050 ( 26) GAGAGGATGGAGTTGT 1 34293 ( 100) GATGGGGGTGAGTTGA 1 10558 ( 340) GTGTTGGTGGATGTGT 1 10025 ( 190) CTGATGGATGAGTTCT 1 3021 ( 268) GTTGTAGTGGTGTTGG 1 263031 ( 2) CTGGATGTTGATTTGA 1 40627 ( 145) GCTGCTGGTGTGTTGT 1 10189 ( 32) GCGTGAGTGGCGTTGT 1 10559 ( 31) CAGATGGAGGTGTGGT 1 34672 ( 48) GTGGTTGTTGTTGCGT 1 10788 ( 287) GTGTTTGTTTGTTTGT 1 20945 ( 121) GCGTAGAGTGCGTCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11640 bayes= 9.43433 E= 3.9e-007 -1097 -27 176 -1097 67 -27 -1097 56 -1097 -1097 166 -12 0 -1097 93 15 26 -227 -66 88 -132 -1097 134 15 -132 -1097 193 -1097 48 -1097 -66 88 -1097 -1097 8 147 -1097 -1097 200 -243 67 -69 -124 37 -1097 -1097 176 -44 -1097 -1097 -124 173 -1097 -69 -224 156 -1097 -227 193 -243 -132 -1097 -24 137 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 3.9e-007 0.000000 0.200000 0.800000 0.000000 0.400000 0.200000 0.000000 0.400000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.450000 0.300000 0.300000 0.050000 0.150000 0.500000 0.100000 0.000000 0.600000 0.300000 0.100000 0.000000 0.900000 0.000000 0.350000 0.000000 0.150000 0.500000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.950000 0.050000 0.400000 0.150000 0.100000 0.350000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.100000 0.900000 0.000000 0.150000 0.050000 0.800000 0.000000 0.050000 0.900000 0.050000 0.100000 0.000000 0.200000 0.700000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][ATC][GT][GTA][TA][GT]G[TA][TG]G[AT][GT]TTG[TG] -------------------------------------------------------------------------------- Time 10.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 20 llr = 217 E-value = 5.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1211:::4::2:2: pos.-specific C 59258:34:18118:: probability G :271:61:a::9::47 matrix T 6:13137616318353 bits 2.1 1.9 * 1.7 * 1.5 * * Relative 1.2 * * ** * Entropy 1.0 ** * ** **** * (15.6 bits) 0.8 ** * *** **** * 0.6 *** ********** * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TCGCCGTTGTCGTCTG consensus C T TCC AT TGT sequence A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25182 26 6.74e-09 CGTCGCGTCG TCGCCTTTGTCGTCGG CCATCACTCG 3098 43 1.17e-07 GGCGGCGGTT TCGTCGTCGTCGTTGG AGGAGGGAAT 10559 268 2.01e-07 TGTCTTTTGG CCGCCGTTGATGTTTG CAGAGATGTT 34672 175 2.29e-07 AGTCATGGCA TCGTCGTCGTCGTCAT CGTCGTCGTC 10189 234 3.40e-07 AAACAAAGGT CCCCCGTTGACGTTTG TTGGCCTTAA 21599 331 6.24e-07 GACGATTGAC TCACCGTTGACGTTTG AGTGTGGATG 24888 321 9.72e-07 AACCCCAAAG CCGCCTCCGTCCTCTG CATTCACTTT 263031 57 1.49e-06 ATGGGAGCGT TCGCAGTTGACGACGG GGGGTTGCTG 23050 158 2.98e-06 GGGAGGCTGC TGGACGTTGACGTCAT GGTATTCACA 10558 43 3.92e-06 CTTGTCTCCC CGTCCGTTGTTGTCGG CGTCGGCGGG 34293 365 4.70e-06 ATCCATATCA CCGACACCGCCGTCTG TCGCCTCAAC 3021 355 6.08e-06 AGAAGGAAGG CCGAATCTGTCGTCTT GTCCATAGTT 20945 188 6.62e-06 TGAACTGATG TCGATGTTGTTGTTGG AGGATCATCT 9203 420 1.16e-05 TGCTTCGCTG CCACCGCTGTCGCCTT CCTACACCTC 25141 399 1.35e-05 TACCTATTCA TCGTCATCTACGTCGG CGCCGGTTCT 269935 356 1.45e-05 TCAGCCGCCG TCGCCTCCGTCCACGT GGAAGTGCTC 40627 164 1.80e-05 GTGTTGTTGG CCTCCGCCGCCGACAG GGTAGCCTCC 1880 122 2.22e-05 AAACATGCAG CCGGCTGTGATGTCTG ACGCACCTCG 6483 143 2.72e-05 GTTTGTAGTG TCCTCTTCGTCTTCTT TCCCACTCTG 10788 249 5.05e-05 GAGTAGCCAT TGCTTGTTGTTGTCAG TCGGCGGCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25182 6.7e-09 25_[+3]_459 3098 1.2e-07 42_[+3]_442 10559 2e-07 267_[+3]_217 34672 2.3e-07 174_[+3]_310 10189 3.4e-07 233_[+3]_251 21599 6.2e-07 330_[+3]_154 24888 9.7e-07 320_[+3]_164 263031 1.5e-06 56_[+3]_428 23050 3e-06 157_[+3]_327 10558 3.9e-06 42_[+3]_442 34293 4.7e-06 364_[+3]_120 3021 6.1e-06 354_[+3]_130 20945 6.6e-06 187_[+3]_297 9203 1.2e-05 419_[+3]_65 25141 1.3e-05 398_[+3]_86 269935 1.5e-05 355_[+3]_129 40627 1.8e-05 163_[+3]_321 1880 2.2e-05 121_[+3]_363 6483 2.7e-05 142_[+3]_342 10788 5.1e-05 248_[+3]_236 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=20 25182 ( 26) TCGCCTTTGTCGTCGG 1 3098 ( 43) TCGTCGTCGTCGTTGG 1 10559 ( 268) CCGCCGTTGATGTTTG 1 34672 ( 175) TCGTCGTCGTCGTCAT 1 10189 ( 234) CCCCCGTTGACGTTTG 1 21599 ( 331) TCACCGTTGACGTTTG 1 24888 ( 321) CCGCCTCCGTCCTCTG 1 263031 ( 57) TCGCAGTTGACGACGG 1 23050 ( 158) TGGACGTTGACGTCAT 1 10558 ( 43) CGTCCGTTGTTGTCGG 1 34293 ( 365) CCGACACCGCCGTCTG 1 3021 ( 355) CCGAATCTGTCGTCTT 1 20945 ( 188) TCGATGTTGTTGTTGG 1 9203 ( 420) CCACCGCTGTCGCCTT 1 25141 ( 399) TCGTCATCTACGTCGG 1 269935 ( 356) TCGCCTCCGTCCACGT 1 40627 ( 164) CCTCCGCCGCCGACAG 1 1880 ( 122) CCGGCTGTGATGTCTG 1 6483 ( 143) TCCTCTTCGTCTTCTT 1 10788 ( 249) TGCTTGTTGTTGTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11640 bayes= 10.6579 E= 5.4e-005 -1097 90 -1097 102 -1097 181 -66 -1097 -132 -69 146 -144 -33 105 -224 -12 -132 173 -1097 -144 -132 -1097 134 15 -1097 31 -224 126 -1097 73 -1097 115 -1097 -1097 200 -243 48 -127 -1097 102 -1097 163 -1097 -12 -1097 -127 184 -243 -74 -227 -1097 156 -1097 163 -1097 -12 -33 -1097 56 73 -1097 -1097 156 15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 5.4e-005 0.000000 0.450000 0.000000 0.550000 0.000000 0.850000 0.150000 0.000000 0.100000 0.150000 0.650000 0.100000 0.200000 0.500000 0.050000 0.250000 0.100000 0.800000 0.000000 0.100000 0.100000 0.000000 0.600000 0.300000 0.000000 0.300000 0.050000 0.650000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.950000 0.050000 0.350000 0.100000 0.000000 0.550000 0.000000 0.750000 0.000000 0.250000 0.000000 0.100000 0.850000 0.050000 0.150000 0.050000 0.000000 0.800000 0.000000 0.750000 0.000000 0.250000 0.200000 0.000000 0.350000 0.450000 0.000000 0.000000 0.700000 0.300000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC]CG[CTA]C[GT][TC][TC]G[TA][CT]GT[CT][TGA][GT] -------------------------------------------------------------------------------- Time 14.76 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10025 1.28e-05 189_[+2(5.43e-06)]_246_\ [+1(1.21e-05)]_16_[+1(8.51e-08)]_1 10189 1.15e-07 31_[+2(1.20e-05)]_186_\ [+3(3.40e-07)]_27_[+1(9.81e-07)]_208 10558 4.32e-05 42_[+3(3.92e-06)]_281_\ [+2(4.99e-06)]_145 10559 1.73e-07 30_[+2(1.29e-05)]_221_\ [+3(2.01e-07)]_185_[+1(2.40e-06)]_16 10788 2.64e-04 248_[+3(5.05e-05)]_22_\ [+2(2.90e-05)]_124_[+1(1.69e-05)]_58 1880 7.96e-04 121_[+3(2.22e-05)]_329_\ [+1(4.00e-06)]_18 20945 2.40e-05 120_[+2(3.28e-05)]_51_\ [+3(6.62e-06)]_218_[+1(7.11e-06)]_63 21599 8.46e-09 196_[+2(1.25e-07)]_29_\ [+1(2.96e-06)]_73_[+3(6.24e-07)]_154 22596 4.61e-09 240_[+2(1.24e-08)]_168_\ [+1(1.11e-05)]_44_[+1(4.37e-08)] 23050 2.33e-05 25_[+2(3.84e-06)]_116_\ [+3(2.98e-06)]_327 23791 8.72e-02 307_[+1(1.11e-05)]_177 23806 6.11e-04 159_[+2(3.50e-06)]_172_\ [+1(1.11e-05)]_137 24888 6.37e-04 157_[+1(3.65e-05)]_147_\ [+3(9.72e-07)]_164 25141 1.63e-06 148_[+1(6.47e-06)]_78_\ [+2(8.56e-07)]_140_[+3(1.35e-05)]_86 25182 2.90e-08 25_[+3(6.74e-09)]_83_[+2(2.92e-06)]_\ 344_[+1(4.52e-05)] 263031 3.13e-06 1_[+2(1.11e-05)]_39_[+3(1.49e-06)]_\ 390_[+1(9.30e-06)]_22 269935 1.36e-05 166_[+2(6.07e-07)]_173_\ [+3(1.45e-05)]_28_[+1(9.35e-05)]_85 3021 9.94e-07 267_[+2(6.41e-06)]_23_\ [+1(1.10e-06)]_32_[+3(6.08e-06)]_130 3098 5.83e-12 42_[+3(1.17e-07)]_91_[+2(3.86e-09)]_\ 89_[+2(1.49e-05)]_115_[+1(2.05e-07)]_51_[+1(2.71e-05)]_9_[+1(6.47e-06)]_7 34293 1.52e-05 1_[+2(9.66e-05)]_82_[+2(4.99e-06)]_\ 147_[+1(3.92e-05)]_86_[+3(4.70e-06)]_120 34672 5.54e-07 47_[+2(1.38e-05)]_67_[+1(7.11e-06)]_\ 28_[+3(2.29e-07)]_310 40627 1.33e-06 144_[+2(1.20e-05)]_3_[+3(1.80e-05)]_\ 284_[+1(2.77e-07)]_21 6483 2.15e-03 142_[+3(2.72e-05)]_313_\ [+1(5.37e-06)]_13 9203 3.06e-09 29_[+2(7.76e-08)]_331_\ [+1(8.51e-08)]_27_[+3(1.16e-05)]_45_[+1(4.85e-05)]_4 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************