******************************************************************************** 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/122/122.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10391 1.0000 500 11176 1.0000 500 11265 1.0000 500 11569 1.0000 500 21299 1.0000 500 21720 1.0000 500 21753 1.0000 500 22430 1.0000 500 240 1.0000 500 24738 1.0000 500 25094 1.0000 500 25391 1.0000 500 25565 1.0000 500 264410 1.0000 500 268460 1.0000 500 270113 1.0000 500 28413 1.0000 500 31232 1.0000 500 31266 1.0000 500 33480 1.0000 500 35390 1.0000 500 36716 1.0000 500 3906 1.0000 500 6893 1.0000 500 6911 1.0000 500 7667 1.0000 500 8706 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/122/122.seqs.fa -oc motifs/122 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.220 G 0.241 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.220 G 0.241 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 13 llr = 192 E-value = 3.7e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::22::1:3:2::::::32 pos.-specific C :11:22::1::21:4::321: probability G 541a31a4:86:48:282828 matrix T 558:45:6821842682515: bits 2.2 2.0 * * 1.7 * * 1.5 * * Relative 1.3 * * * * * ** * Entropy 1.1 ** **** * **** * * (21.3 bits) 0.9 * ** **** * **** * * 0.7 **** ****** **** * * 0.4 **** ****** ****** * 0.2 **** **************** 0.0 --------------------- Multilevel TTTGTTGTTGGTGGTTGTGTG consensus GG GA G A T C C AA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 240 261 6.97e-10 ACGCTTCATC GTTGGTGGTGATTGCTGTGAG CCGAAGAGAG 11569 334 1.69e-09 TGGCTACCAT GTTGTTGTTTGTTGTTGCGAG CTGGAGGTGA 10391 67 2.56e-09 GTTGGGTGGG TTTGGTGTTGTTGGTTGGGTG GCTGAGGGCT 31266 323 2.31e-08 TTGGATTCGG TGTGTCGTTGATGGTTGTTTG AGATTGATTT 22430 362 4.16e-08 GGTGTGTTGG TTGGTTGGTGGTGGCTGGCTG ACAAGGACCT 35390 201 6.00e-08 GTGTTCGTGT TGTGGTGTAGATGTTTGTGTG TTCGATTGAC 21299 304 6.00e-08 GACGGTTGCT GGTGCTGTTGACTGCGGTGTG TGAAGAGAGA 7667 34 7.81e-08 GCTGAGAAGT TGTGCAGGTTGCTGTTGTGTG TCTGTATCCA 11176 357 1.39e-07 CCCAAATGGC TTTGGAGTCGGTAGCTGTGAA TCAATCTCCT 25565 375 1.51e-07 TTGCGGCGGC GTTGTTGGTGGTATTTTCGGG AGTTTGGCCT 21753 253 3.88e-07 TTGTGGAAGG TCTGTGGTTGGTCGTTGGGCG AGCCCAACTT 264410 191 4.15e-07 AAATCATCAC GTTGACGTTGGTTGTTTCCAA CGACAAAAGG 21720 19 1.28e-06 GTGTTGAGAA GGCGAAGGTGGTGGCGGCGGA ACGACCAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 240 7e-10 260_[+1]_219 11569 1.7e-09 333_[+1]_146 10391 2.6e-09 66_[+1]_413 31266 2.3e-08 322_[+1]_157 22430 4.2e-08 361_[+1]_118 35390 6e-08 200_[+1]_279 21299 6e-08 303_[+1]_176 7667 7.8e-08 33_[+1]_446 11176 1.4e-07 356_[+1]_123 25565 1.5e-07 374_[+1]_105 21753 3.9e-07 252_[+1]_227 264410 4.1e-07 190_[+1]_289 21720 1.3e-06 18_[+1]_461 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=13 240 ( 261) GTTGGTGGTGATTGCTGTGAG 1 11569 ( 334) GTTGTTGTTTGTTGTTGCGAG 1 10391 ( 67) TTTGGTGTTGTTGGTTGGGTG 1 31266 ( 323) TGTGTCGTTGATGGTTGTTTG 1 22430 ( 362) TTGGTTGGTGGTGGCTGGCTG 1 35390 ( 201) TGTGGTGTAGATGTTTGTGTG 1 21299 ( 304) GGTGCTGTTGACTGCGGTGTG 1 7667 ( 34) TGTGCAGGTTGCTGTTGTGTG 1 11176 ( 357) TTTGGAGTCGGTAGCTGTGAA 1 25565 ( 375) GTTGTTGGTGGTATTTTCGGG 1 21753 ( 253) TCTGTGGTTGGTCGTTGGGCG 1 264410 ( 191) GTTGACGTTGGTTGTTTCCAA 1 21720 ( 19) GGCGAAGGTGGTGGCGGCGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.4909 E= 3.7e-006 -1035 -1035 94 100 -1035 -151 67 100 -1035 -151 -164 165 -1035 -1035 205 -1035 -81 -52 35 52 -23 -52 -164 100 -1035 -1035 205 -1035 -1035 -1035 67 119 -181 -151 -1035 165 -1035 -1035 181 -81 19 -1035 135 -180 -1035 -52 -1035 165 -81 -151 67 52 -1035 -1035 181 -81 -1035 80 -1035 119 -1035 -1035 -65 165 -1035 -1035 181 -81 -1035 48 -6 78 -1035 -52 167 -180 19 -151 -65 78 -23 -1035 167 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 3.7e-006 0.000000 0.000000 0.461538 0.538462 0.000000 0.076923 0.384615 0.538462 0.000000 0.076923 0.076923 0.846154 0.000000 0.000000 1.000000 0.000000 0.153846 0.153846 0.307692 0.384615 0.230769 0.153846 0.076923 0.538462 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.384615 0.615385 0.076923 0.076923 0.000000 0.846154 0.000000 0.000000 0.846154 0.153846 0.307692 0.000000 0.615385 0.076923 0.000000 0.153846 0.000000 0.846154 0.153846 0.076923 0.384615 0.384615 0.000000 0.000000 0.846154 0.153846 0.000000 0.384615 0.000000 0.615385 0.000000 0.000000 0.153846 0.846154 0.000000 0.000000 0.846154 0.153846 0.000000 0.307692 0.230769 0.461538 0.000000 0.153846 0.769231 0.076923 0.307692 0.076923 0.153846 0.461538 0.230769 0.000000 0.769231 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][TG]TG[TG][TA]G[TG]TG[GA]T[GT]G[TC]TG[TCG]G[TA][GA] -------------------------------------------------------------------------------- Time 7.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 14 llr = 171 E-value = 6.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4:::44:615::11: pos.-specific C a446a4:84641a669 probability G :::::1::12:2::11 matrix T :364:162::16:22: 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 CATCCCTCACATCCCC consensus CCT AATCGCG TT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 35390 424 5.20e-08 ACCATCACAT CATCCTACCCATCCCC CATCCATTCC 25094 459 6.94e-08 GAACGATCTA CACCCCACACCGCCCC TGTCATCTCT 11569 228 6.94e-08 GTCTTTCTCG CCTTCATCACATCTCC GCCGAGGAAG 11265 252 1.54e-07 ACCTGCAAAT CTTCCCACAACTCCCC AAAACACACT 10391 419 1.54e-07 GCCAACATAA CCCCCCTCACTCCCCC CCCTCAAATG 25565 96 2.56e-07 TCAAACTCCT CATCCCTTCCCTCCTC ATCACAAACC 22430 200 3.61e-07 ATGCTTTCTT CCTCCGTCACATCACC GTGTGATACA 33480 478 1.58e-06 CTGTCGTCGT CACCCATCAGCTCTTC TAGTAGG 8706 411 1.72e-06 TGAACTCCAC CTCCCCTCCGACCTCC GTTTCATCTA 36716 432 2.20e-06 ATAGCCACAG CCTCCAATACAGCACC CGAACGTCGG 31232 44 4.54e-06 CGCTCCAATT CTTTCTTCCCTTCCGC TTCCCACAAT 6893 465 5.17e-06 CAAAGCAAAA CACTCAACAGAGCCAC TAAGCTGATT 264410 317 6.58e-06 TGCGTCCATA CTTTCATTGCATCCAC TTTGTTGTCG 11176 53 7.38e-06 TTGTTGTTCT CCTTCCTCCACTCCTG ACCCCAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35390 5.2e-08 423_[+2]_61 25094 6.9e-08 458_[+2]_26 11569 6.9e-08 227_[+2]_257 11265 1.5e-07 251_[+2]_233 10391 1.5e-07 418_[+2]_66 25565 2.6e-07 95_[+2]_389 22430 3.6e-07 199_[+2]_285 33480 1.6e-06 477_[+2]_7 8706 1.7e-06 410_[+2]_74 36716 2.2e-06 431_[+2]_53 31232 4.5e-06 43_[+2]_441 6893 5.2e-06 464_[+2]_20 264410 6.6e-06 316_[+2]_168 11176 7.4e-06 52_[+2]_432 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=14 35390 ( 424) CATCCTACCCATCCCC 1 25094 ( 459) CACCCCACACCGCCCC 1 11569 ( 228) CCTTCATCACATCTCC 1 11265 ( 252) CTTCCCACAACTCCCC 1 10391 ( 419) CCCCCCTCACTCCCCC 1 25565 ( 96) CATCCCTTCCCTCCTC 1 22430 ( 200) CCTCCGTCACATCACC 1 33480 ( 478) CACCCATCAGCTCTTC 1 8706 ( 411) CTCCCCTCCGACCTCC 1 36716 ( 432) CCTCCAATACAGCACC 1 31232 ( 44) CTTTCTTCCCTTCCGC 1 6893 ( 465) CACTCAACAGAGCCAC 1 264410 ( 317) CTTTCATTGCATCCAC 1 11176 ( 53) CCTTCCTCCACTCCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13095 bayes= 11.5387 E= 6.1e-002 -1045 218 -1045 -1045 40 70 -1045 9 -1045 70 -1045 126 -1045 155 -1045 41 -1045 218 -1045 -1045 40 96 -175 -91 40 -1045 -1045 126 -1045 183 -1045 -33 108 70 -175 -1045 -92 155 -17 -1045 89 70 -1045 -91 -1045 -62 -17 126 -1045 218 -1045 -1045 -92 155 -1045 -33 -92 138 -175 -33 -1045 208 -175 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 14 E= 6.1e-002 0.000000 1.000000 0.000000 0.000000 0.357143 0.357143 0.000000 0.285714 0.000000 0.357143 0.000000 0.642857 0.000000 0.642857 0.000000 0.357143 0.000000 1.000000 0.000000 0.000000 0.357143 0.428571 0.071429 0.142857 0.357143 0.000000 0.000000 0.642857 0.000000 0.785714 0.000000 0.214286 0.571429 0.357143 0.071429 0.000000 0.142857 0.642857 0.214286 0.000000 0.500000 0.357143 0.000000 0.142857 0.000000 0.142857 0.214286 0.642857 0.000000 1.000000 0.000000 0.000000 0.142857 0.642857 0.000000 0.214286 0.142857 0.571429 0.071429 0.214286 0.000000 0.928571 0.071429 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[ACT][TC][CT]C[CA][TA][CT][AC][CG][AC][TG]C[CT][CT]C -------------------------------------------------------------------------------- Time 15.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 27 llr = 274 E-value = 1.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 22:34365132::5:71363: pos.-specific C ::1::1:1::::1:1:4:::: probability G 7664454167465293373:9 matrix T :23221:32:4333::3:171 bits 2.2 2.0 1.7 * 1.5 * Relative 1.3 * * Entropy 1.1 * ** * (14.7 bits) 0.9 * * * * ** * ** 0.7 * * * ** * ** **** 0.4 *** * * ******** **** 0.2 ********************* 0.0 --------------------- Multilevel GGGGGGAAGGGGGAGACGATG consensus AATAAAGTTATTTT GGAGA sequence T A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6911 318 1.89e-09 GAGGAGAATG GGGAGAGAGGGGGGGAGGATG CAGTTGTCCA 33480 392 1.89e-08 AGCTGTTCGG GGGGGGGGGGGGGTGACGAAG TGTCTAGACT 6893 86 9.29e-08 CTTACGCTGT GGTGTAAAAGGGTAGACGATG ATAAATAAGC 7667 80 2.83e-07 ATGTCGTCAT GTTGTGATGGTTGAGATGATG AATCGTTGTA 11569 248 2.83e-07 ATCTCCGCCG AGGAAGAAGAGGGAGGTAATG ACGGGAGCAA 22430 335 3.23e-07 AGTGATGGGT GGTTGGGAGAGGCAGACGGTG TGTTGGTTGG 25565 326 6.82e-07 AAGTTGTGGA AGGGAGACGGGTTGGGTGATG CCCAGATGTT 3906 177 9.71e-07 TGTTCGTACG GGCGGAAAGGAGGAGAAGAAG GATGCAGTTC 11176 181 2.60e-06 AAATCAACAA GGGGATAAAGAGCTGACAATG TACGAATAAA 35390 79 3.90e-06 GTTTGCCATG GAGTTGACGGTGGAGGCATTG GCTTGGGATA 10391 374 4.31e-06 AATAGTTATT GGGGAGATGAAGGAGACAAAT AATAGCACCA 240 133 5.23e-06 AATACTCGAG TTGATGGAAGTGGAGACGATG ACTGCAGTAA 28413 197 5.75e-06 ATGACGGTAC GATGTGATTGATTTGATGATG AAATCAAAAT 31232 264 6.94e-06 GATTAACAGT GAGAGGAAGGTTATGGGGTTG CCCTCGGGCA 31266 281 8.33e-06 ACACCATCAG AAGCAAGAGGGGGGGGGGGTG TTTTCTCGTC 25094 131 9.12e-06 GTCAGGATTA GGGAAAAAGGAGTTGAGAGAT CAAAGTCCGC 21753 314 9.12e-06 AAAACTCTCA GGGGGGGGGATTGGCGGGGTG AGAGGGTTGA 21720 310 1.09e-05 AGCAGAAGAG GAGAGAATGGGGCAGGGCGTG GACGTCGACA 21299 221 1.09e-05 TGTTTTGCTC GTGGTGATTGTGTAGGAGGAG GTATGCAGCA 270113 43 1.41e-05 TTACCAGGCA GGTGACGATGGTGATGCGATG GTACGTCAAT 264410 419 1.53e-05 GATAGTTTTC GGCAACACGGTTTTGAGGTTG GATCAATCTG 268460 191 2.70e-05 GATAACAGTC GTGAGCCTTGTTGTGATGATG TTGTGTAGAG 8706 211 3.66e-05 TTCGAGGAGG GCGTGAAAGAGGTGCACGAAG CAAGCGTTGA 36716 198 4.25e-05 GACTCTTTCG AGGAAGGCATTGGAGAGAGTG CCTCATGATG 25391 179 8.50e-05 CATCATTCTC ATTGATAAGAAGTAGATAGAG GGATCTGCTT 24738 81 1.79e-04 GGTTGATAGT AGATGAGTTAGTTTGATGGTG CATTGGCTAT 11265 170 6.41e-04 ATCATTCTTG GATTGTGATGTCGTCACGACG ATCCTTGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6911 1.9e-09 317_[+3]_162 33480 1.9e-08 391_[+3]_88 6893 9.3e-08 85_[+3]_394 7667 2.8e-07 79_[+3]_400 11569 2.8e-07 247_[+3]_232 22430 3.2e-07 334_[+3]_145 25565 6.8e-07 325_[+3]_154 3906 9.7e-07 176_[+3]_303 11176 2.6e-06 180_[+3]_299 35390 3.9e-06 78_[+3]_401 10391 4.3e-06 373_[+3]_106 240 5.2e-06 132_[+3]_347 28413 5.8e-06 196_[+3]_283 31232 6.9e-06 263_[+3]_216 31266 8.3e-06 280_[+3]_199 25094 9.1e-06 130_[+3]_349 21753 9.1e-06 313_[+3]_166 21720 1.1e-05 309_[+3]_170 21299 1.1e-05 220_[+3]_259 270113 1.4e-05 42_[+3]_437 264410 1.5e-05 418_[+3]_61 268460 2.7e-05 190_[+3]_289 8706 3.7e-05 210_[+3]_269 36716 4.2e-05 197_[+3]_282 25391 8.5e-05 178_[+3]_301 24738 0.00018 80_[+3]_399 11265 0.00064 169_[+3]_310 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=27 6911 ( 318) GGGAGAGAGGGGGGGAGGATG 1 33480 ( 392) GGGGGGGGGGGGGTGACGAAG 1 6893 ( 86) GGTGTAAAAGGGTAGACGATG 1 7667 ( 80) GTTGTGATGGTTGAGATGATG 1 11569 ( 248) AGGAAGAAGAGGGAGGTAATG 1 22430 ( 335) GGTTGGGAGAGGCAGACGGTG 1 25565 ( 326) AGGGAGACGGGTTGGGTGATG 1 3906 ( 177) GGCGGAAAGGAGGAGAAGAAG 1 11176 ( 181) GGGGATAAAGAGCTGACAATG 1 35390 ( 79) GAGTTGACGGTGGAGGCATTG 1 10391 ( 374) GGGGAGATGAAGGAGACAAAT 1 240 ( 133) TTGATGGAAGTGGAGACGATG 1 28413 ( 197) GATGTGATTGATTTGATGATG 1 31232 ( 264) GAGAGGAAGGTTATGGGGTTG 1 31266 ( 281) AAGCAAGAGGGGGGGGGGGTG 1 25094 ( 131) GGGAAAAAGGAGTTGAGAGAT 1 21753 ( 314) GGGGGGGGGATTGGCGGGGTG 1 21720 ( 310) GAGAGAATGGGGCAGGGCGTG 1 21299 ( 221) GTGGTGATTGTGTAGGAGGAG 1 270113 ( 43) GGTGACGATGGTGATGCGATG 1 264410 ( 419) GGCAACACGGTTTTGAGGTTG 1 268460 ( 191) GTGAGCCTTGTTGTGATGATG 1 8706 ( 211) GCGTGAAAGAGGTGCACGAAG 1 36716 ( 198) AGGAAGGCATTGGAGAGAGTG 1 25391 ( 179) ATTGATAAGAAGTAGATAGAG 1 24738 ( 81) AGATGAGTTAGTTTGATGGTG 1 11265 ( 170) GATTGTGATGTCGTCACGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 8.90388 E= 1.8e-003 -28 -1140 162 -286 -28 -257 121 -54 -286 -157 139 -5 30 -257 88 -54 46 -1140 76 -28 13 -99 100 -127 113 -257 62 -1140 94 -57 -170 -5 -87 -1140 139 -28 -6 -1140 155 -286 -28 -1140 76 46 -1140 -257 139 31 -286 -99 111 31 83 -1140 -38 31 -1140 -99 182 -286 130 -1140 47 -1140 -186 75 30 -5 -6 -257 155 -1140 104 -1140 47 -127 -6 -257 -1140 139 -1140 -1140 194 -186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 1.8e-003 0.222222 0.000000 0.740741 0.037037 0.222222 0.037037 0.555556 0.185185 0.037037 0.074074 0.629630 0.259259 0.333333 0.037037 0.444444 0.185185 0.370370 0.000000 0.407407 0.222222 0.296296 0.111111 0.481481 0.111111 0.592593 0.037037 0.370370 0.000000 0.518519 0.148148 0.074074 0.259259 0.148148 0.000000 0.629630 0.222222 0.259259 0.000000 0.703704 0.037037 0.222222 0.000000 0.407407 0.370370 0.000000 0.037037 0.629630 0.333333 0.037037 0.111111 0.518519 0.333333 0.481481 0.000000 0.185185 0.333333 0.000000 0.111111 0.851852 0.037037 0.666667 0.000000 0.333333 0.000000 0.074074 0.370370 0.296296 0.259259 0.259259 0.037037 0.703704 0.000000 0.555556 0.000000 0.333333 0.111111 0.259259 0.037037 0.000000 0.703704 0.000000 0.000000 0.925926 0.074074 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][GA][GT][GA][GAT][GA][AG][AT][GT][GA][GTA][GT][GT][AT]G[AG][CGT][GA][AG][TA]G -------------------------------------------------------------------------------- Time 22.26 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10391 8.72e-11 66_[+1(2.56e-09)]_286_\ [+3(4.31e-06)]_24_[+2(1.54e-07)]_66 11176 7.86e-08 52_[+2(7.38e-06)]_112_\ [+3(2.60e-06)]_155_[+1(1.39e-07)]_123 11265 7.49e-04 251_[+2(1.54e-07)]_233 11569 2.18e-12 227_[+2(6.94e-08)]_4_[+3(2.83e-07)]_\ 65_[+1(1.69e-09)]_146 21299 1.59e-05 68_[+1(2.93e-05)]_131_\ [+3(1.09e-05)]_62_[+1(6.00e-08)]_176 21720 1.88e-04 18_[+1(1.28e-06)]_270_\ [+3(1.09e-05)]_170 21753 2.31e-05 252_[+1(3.88e-07)]_40_\ [+3(9.12e-06)]_166 22430 2.32e-10 199_[+2(3.61e-07)]_119_\ [+3(3.23e-07)]_6_[+1(4.16e-08)]_118 240 1.85e-07 132_[+3(5.23e-06)]_107_\ [+1(6.97e-10)]_219 24738 4.64e-01 500 25094 3.18e-06 130_[+3(9.12e-06)]_307_\ [+2(6.94e-08)]_26 25391 1.95e-01 178_[+3(8.50e-05)]_301 25565 1.12e-09 62_[+2(7.87e-05)]_17_[+2(2.56e-07)]_\ 214_[+3(6.82e-07)]_28_[+1(1.51e-07)]_56_[+1(4.54e-05)]_28 264410 9.50e-07 190_[+1(4.15e-07)]_105_\ [+2(6.58e-06)]_86_[+3(1.53e-05)]_61 268460 4.32e-02 190_[+3(2.70e-05)]_289 270113 5.82e-03 42_[+3(1.41e-05)]_380_\ [+2(4.26e-05)]_41 28413 1.48e-02 196_[+3(5.75e-06)]_283 31232 2.45e-04 43_[+2(4.54e-06)]_204_\ [+3(6.94e-06)]_216 31266 2.99e-06 280_[+3(8.33e-06)]_21_\ [+1(2.31e-08)]_157 33480 1.19e-07 391_[+3(1.89e-08)]_65_\ [+2(1.58e-06)]_7 35390 5.47e-10 36_[+1(4.54e-05)]_21_[+3(3.90e-06)]_\ 42_[+1(1.96e-05)]_38_[+1(6.00e-08)]_202_[+2(5.20e-08)]_61 36716 9.19e-04 197_[+3(4.25e-05)]_213_\ [+2(2.20e-06)]_53 3906 5.60e-03 176_[+3(9.71e-07)]_303 6893 9.66e-06 85_[+3(9.29e-08)]_358_\ [+2(5.17e-06)]_20 6911 1.31e-06 256_[+3(7.96e-05)]_19_\ [+3(1.19e-05)]_[+3(1.89e-09)]_162 7667 5.10e-07 33_[+1(7.81e-08)]_25_[+3(2.83e-07)]_\ 400 8706 3.79e-04 210_[+3(3.66e-05)]_179_\ [+2(1.72e-06)]_74 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************