******************************************************************************** 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/360/360.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11841 1.0000 500 11842 1.0000 500 1440 1.0000 500 17623 1.0000 500 17687 1.0000 500 20827 1.0000 500 20829 1.0000 500 21143 1.0000 500 21623 1.0000 500 22197 1.0000 500 22198 1.0000 500 22720 1.0000 500 23657 1.0000 500 24172 1.0000 500 24341 1.0000 500 25299 1.0000 500 25478 1.0000 500 262125 1.0000 500 269274 1.0000 500 269297 1.0000 500 26941 1.0000 500 27414 1.0000 500 3393 1.0000 500 33968 1.0000 500 37980 1.0000 500 39516 1.0000 500 4067 1.0000 500 42660 1.0000 500 5394 1.0000 500 6370 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/360/360.seqs.fa -oc motifs/360 -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= 30 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= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.238 G 0.237 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.238 G 0.237 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 25 llr = 245 E-value = 1.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::2:a8:25 pos.-specific C 83:981:::162 probability G :12::6a:29:1 matrix T 26812:::::23 bits 2.1 * 1.9 * 1.7 ** * 1.5 * ** * Relative 1.2 * *** **** Entropy 1.0 * *** **** (14.1 bits) 0.8 * ******** 0.6 *********** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel CTTCCGGAAGCA consensus CG TA G TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 23657 374 1.06e-07 CTTCCATCAA CTTCCGGAAGCT ATTACTCGTA 25478 399 4.17e-07 AGCGGGAAAA CTTCCGGAGGCA TTACACCACC 21143 381 4.17e-07 CTGCTTCGAG CTTCCAGAAGCA GGACCCTAAT 39516 281 1.19e-06 TCGCTTTTCT CTTCCCGAAGCA AGAAGCAGGT 20827 355 1.53e-06 CTTTGTTAGT CTTCCAGAAGTA GTGTCAACAA 26941 85 1.98e-06 TAGGGTCCTG CTTCTGGAAGCT CGAAGCAGCC 22198 423 1.98e-06 CTCGTCACCA CTTCCAGAGGCA AAAACTTCGA 24172 438 3.52e-06 GCGTGAGCCG CTTCCGGAGGTT GGATGGAGCG 27414 266 5.04e-06 AAAGATACCT TTGCCGGAAGCA ACGTCCTTTT 269274 416 5.97e-06 CACCTCGGCT CTTCCGGAACCT CACTTCCGCC 5394 247 6.96e-06 GCAACTCCTT CCTCTGGAAGTA TCTTTCCCGT 269297 168 7.98e-06 AAGGTATCCT CCGCCGGAAGTT GCCTCTGTTC 25299 374 7.98e-06 CCAACATCTC TTTCCGGAAGAA CCAAGCTGGA 1440 395 9.14e-06 CAGCCTCCTC CCTCCGGAGGCG GTAAAAGCGA 22720 423 1.06e-05 GGGAAAGATA CTTCCAGAGGAA GGAGTTGCAG 37980 438 1.41e-05 TTGCCGGTTG CTGCCCGAAGCC AGAGGCAACG 42660 234 1.75e-05 GTCGGTCGGT CGGCTGGAAGCA AGTTATATGA 3393 78 3.19e-05 CGCCATTTAA CGTCCGGCAGCA GCCTCTTCCT 22197 252 3.46e-05 GAAGTTTTTG CCTCTGGAAGTG GTGACGAGCA 6370 346 4.04e-05 CTTCAATGGC TTTTCGGAAGCC CCATACCATA 11842 211 5.65e-05 CAAAGGATAC CTTCCAGAACAT GTCGGACTTA 262125 200 6.89e-05 GGGAGCGCTT CCGCCAGAGGTC TTCTCCTCTT 24341 268 8.68e-05 TATACGTTGA TCTTTGGAAGCA AAGCTTCATT 17623 383 1.16e-04 TTGTTCCCTA CCGTCCGAAGCC ACCAACTTCC 21623 125 1.24e-04 ATCCAGAAGT AGTCCGGAAGAT ACCTTTTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23657 1.1e-07 373_[+1]_115 25478 4.2e-07 398_[+1]_90 21143 4.2e-07 380_[+1]_108 39516 1.2e-06 280_[+1]_208 20827 1.5e-06 354_[+1]_134 26941 2e-06 84_[+1]_404 22198 2e-06 422_[+1]_66 24172 3.5e-06 437_[+1]_51 27414 5e-06 265_[+1]_223 269274 6e-06 415_[+1]_73 5394 7e-06 246_[+1]_242 269297 8e-06 167_[+1]_321 25299 8e-06 373_[+1]_115 1440 9.1e-06 394_[+1]_94 22720 1.1e-05 422_[+1]_66 37980 1.4e-05 437_[+1]_51 42660 1.8e-05 233_[+1]_255 3393 3.2e-05 77_[+1]_411 22197 3.5e-05 251_[+1]_237 6370 4e-05 345_[+1]_143 11842 5.6e-05 210_[+1]_278 262125 6.9e-05 199_[+1]_289 24341 8.7e-05 267_[+1]_221 17623 0.00012 382_[+1]_106 21623 0.00012 124_[+1]_364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=25 23657 ( 374) CTTCCGGAAGCT 1 25478 ( 399) CTTCCGGAGGCA 1 21143 ( 381) CTTCCAGAAGCA 1 39516 ( 281) CTTCCCGAAGCA 1 20827 ( 355) CTTCCAGAAGTA 1 26941 ( 85) CTTCTGGAAGCT 1 22198 ( 423) CTTCCAGAGGCA 1 24172 ( 438) CTTCCGGAGGTT 1 27414 ( 266) TTGCCGGAAGCA 1 269274 ( 416) CTTCCGGAACCT 1 5394 ( 247) CCTCTGGAAGTA 1 269297 ( 168) CCGCCGGAAGTT 1 25299 ( 374) TTTCCGGAAGAA 1 1440 ( 395) CCTCCGGAGGCG 1 22720 ( 423) CTTCCAGAGGAA 1 37980 ( 438) CTGCCCGAAGCC 1 42660 ( 234) CGGCTGGAAGCA 1 3393 ( 78) CGTCCGGCAGCA 1 22197 ( 252) CCTCTGGAAGTG 1 6370 ( 346) TTTTCGGAAGCC 1 11842 ( 211) CTTCCAGAACAT 1 262125 ( 200) CCGCCAGAGGTC 1 24341 ( 268) TCTTTGGAAGCA 1 17623 ( 383) CCGTCCGAAGCC 1 21623 ( 125) AGTCCGGAAGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 14670 bayes= 9.68502 E= 1.3e-009 -271 175 -1129 -71 -1129 23 -98 120 -1129 -1129 2 154 -1129 189 -1129 -112 -1129 175 -1129 -39 -13 -99 143 -1129 -1129 -1129 207 -1129 187 -257 -1129 -1129 153 -1129 2 -1129 -1129 -157 195 -1129 -72 133 -1129 -12 87 -57 -157 10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 25 E= 1.3e-009 0.040000 0.800000 0.000000 0.160000 0.000000 0.280000 0.120000 0.600000 0.000000 0.000000 0.240000 0.760000 0.000000 0.880000 0.000000 0.120000 0.000000 0.800000 0.000000 0.200000 0.240000 0.120000 0.640000 0.000000 0.000000 0.000000 1.000000 0.000000 0.960000 0.040000 0.000000 0.000000 0.760000 0.000000 0.240000 0.000000 0.000000 0.080000 0.920000 0.000000 0.160000 0.600000 0.000000 0.240000 0.480000 0.160000 0.080000 0.280000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[TC][TG]C[CT][GA]GA[AG]G[CT][AT] -------------------------------------------------------------------------------- Time 8.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 24 llr = 275 E-value = 5.2e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :62:a3:3543:543:24:77 pos.-specific C :11::::3:12:23:31:::2 probability G 922a:3a34428134452a2: matrix T 115::4:1:1423:3424::1 bits 2.1 * 1.9 ** * * 1.7 * ** * * 1.5 * ** * * Relative 1.2 * ** * * * Entropy 1.0 * ** * * * (16.5 bits) 0.8 * ** * * * *** 0.6 * ** * * * *** 0.4 ** **** * * * * *** 0.2 ********** ********** 0.0 --------------------- Multilevel GATGATGAAATGAAGGGTGAA consensus G CGGATTGTT A G sequence A G C CAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20829 290 7.66e-09 TTGTCCATGA GAGGATGAAACGAAGCGAGAA TTGCAGGAGA 269274 340 1.15e-08 CTTGCTTCGA GAAGATGGAGGGAGGTGAGAA ACTGTAATCT 25299 406 7.20e-08 GGATGAAGAT GACGATGAGAAGAGGTGTGGA CGGGGTGAAA 42660 113 1.94e-07 TGCGGTTGCT GTTGATGGGAGGCGTTGAGAA TGAGAATGCT 27414 193 3.23e-07 GAGACTACAA GAGGAGGAAGTTACGGGAGGA CAGGAAGAGG 37980 368 4.64e-07 GCCTGACGAT GATGATGCACCGAAATTGGAA TTTGACTGGC 26941 1 5.84e-07 . GAGGAAGGAAGGAATCTGGAA TCTCTCGTTT 21143 1 5.84e-07 . GGTGATGGAAAGACTCGCGAA TGGAGTTGAT 22720 95 6.54e-07 AGAGGGCCAT GATGAGGCAGATTACGGTGAA CTGTTGGCGG 3393 276 8.15e-07 GTTAGTGATG GGTGATGCGATGGATGGTGAT CATGATGGAT 24172 268 9.08e-07 CGATGTATGC TATGAGGCAGCGTGGGGAGGA ATTGCTGCGT 22198 59 1.01e-06 AGCAGCAGCG GATGAGGAGACGAGTTGTGTC AGAGCTGATC 11842 17 1.01e-06 CGTCTGAAGA GATGAAGCGATTTGGCTGGAA TTACTAAGTT 1440 250 4.14e-06 GAGATGGGGG GAAGAGGAATTGTAGGCAGAT CATGTCCAAT 5394 274 5.31e-06 CCCGTAAATA GCAGATGGAACGTCACGTGAC ATGTGACAAG 22197 86 5.31e-06 ACCATTGGTA GGTGATGGGTTGCGTGATGAT GCACCGACGA 39516 77 7.85e-06 TTCTTCTATT GATAATGATATGTGATGAGAA AGTGAAATAA 33968 389 7.85e-06 GTTGCATCTT TGCGAGGCGGAGAAGGCAGAA GATTTGATTT 25478 258 9.11e-06 TGAAAGCAAA GATGAAGGACTGCAAGAAGCA GATAATGAAA 23657 223 9.11e-06 GCTGGATGAG GACGAAGCGGAGGCTTCTGAC ATCTTGTTGC 17623 232 9.11e-06 ACAGAAGGAA GAAGAGGAAGATACTTTTGGC CTCCGGACCT 4067 283 1.21e-05 GCCTCCACTT GTTGAGGTGGTTCCAGATGAA TGCTTCAGAT 24341 173 1.30e-05 AAGGCGGTGG GTGGAAGTGGTGAAGTAGGGA TGAATTCACC 20827 174 1.93e-05 GTTTGCGCGG GCTGAAAAATGGAAACGTGAA AGGTATCTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20829 7.7e-09 289_[+2]_190 269274 1.1e-08 339_[+2]_140 25299 7.2e-08 405_[+2]_74 42660 1.9e-07 112_[+2]_367 27414 3.2e-07 192_[+2]_287 37980 4.6e-07 367_[+2]_112 26941 5.8e-07 [+2]_479 21143 5.8e-07 [+2]_479 22720 6.5e-07 94_[+2]_385 3393 8.1e-07 275_[+2]_204 24172 9.1e-07 267_[+2]_212 22198 1e-06 58_[+2]_421 11842 1e-06 16_[+2]_463 1440 4.1e-06 249_[+2]_230 5394 5.3e-06 273_[+2]_206 22197 5.3e-06 85_[+2]_394 39516 7.9e-06 76_[+2]_403 33968 7.9e-06 388_[+2]_91 25478 9.1e-06 257_[+2]_222 23657 9.1e-06 222_[+2]_257 17623 9.1e-06 231_[+2]_248 4067 1.2e-05 282_[+2]_197 24341 1.3e-05 172_[+2]_307 20827 1.9e-05 173_[+2]_306 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=24 20829 ( 290) GAGGATGAAACGAAGCGAGAA 1 269274 ( 340) GAAGATGGAGGGAGGTGAGAA 1 25299 ( 406) GACGATGAGAAGAGGTGTGGA 1 42660 ( 113) GTTGATGGGAGGCGTTGAGAA 1 27414 ( 193) GAGGAGGAAGTTACGGGAGGA 1 37980 ( 368) GATGATGCACCGAAATTGGAA 1 26941 ( 1) GAGGAAGGAAGGAATCTGGAA 1 21143 ( 1) GGTGATGGAAAGACTCGCGAA 1 22720 ( 95) GATGAGGCAGATTACGGTGAA 1 3393 ( 276) GGTGATGCGATGGATGGTGAT 1 24172 ( 268) TATGAGGCAGCGTGGGGAGGA 1 22198 ( 59) GATGAGGAGACGAGTTGTGTC 1 11842 ( 17) GATGAAGCGATTTGGCTGGAA 1 1440 ( 250) GAAGAGGAATTGTAGGCAGAT 1 5394 ( 274) GCAGATGGAACGTCACGTGAC 1 22197 ( 86) GGTGATGGGTTGCGTGATGAT 1 39516 ( 77) GATAATGATATGTGATGAGAA 1 33968 ( 389) TGCGAGGCGGAGAAGGCAGAA 1 25478 ( 258) GATGAAGGACTGCAAGAAGCA 1 23657 ( 223) GACGAAGCGGAGGCTTCTGAC 1 17623 ( 232) GAAGAGGAAGATACTTTTGGC 1 4067 ( 283) GTTGAGGTGGTTCCAGATGAA 1 24341 ( 173) GTGGAAGTGGTGAAGTAGGGA 1 20827 ( 174) GCTGAAAAATGGAAACGTGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 9.67451 E= 5.2e-009 -1123 -1123 195 -165 125 -151 -51 -106 -66 -93 -51 105 -266 -1123 201 -1123 193 -1123 -1123 -1123 -7 -1123 49 67 -266 -1123 201 -1123 34 29 30 -165 104 -1123 81 -265 66 -151 66 -106 -7 -19 -51 52 -1123 -1123 174 -33 93 -51 -151 -7 66 7 49 -1123 -7 -251 66 35 -1123 7 66 52 -66 -93 119 -65 51 -251 -51 67 -1123 -1123 207 -1123 143 -251 -19 -265 143 -51 -1123 -106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 5.2e-009 0.000000 0.000000 0.916667 0.083333 0.625000 0.083333 0.166667 0.125000 0.166667 0.125000 0.166667 0.541667 0.041667 0.000000 0.958333 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.333333 0.416667 0.041667 0.000000 0.958333 0.000000 0.333333 0.291667 0.291667 0.083333 0.541667 0.000000 0.416667 0.041667 0.416667 0.083333 0.375000 0.125000 0.250000 0.208333 0.166667 0.375000 0.000000 0.000000 0.791667 0.208333 0.500000 0.166667 0.083333 0.250000 0.416667 0.250000 0.333333 0.000000 0.250000 0.041667 0.375000 0.333333 0.000000 0.250000 0.375000 0.375000 0.166667 0.125000 0.541667 0.166667 0.375000 0.041667 0.166667 0.416667 0.000000 0.000000 1.000000 0.000000 0.708333 0.041667 0.208333 0.041667 0.708333 0.166667 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GATGA[TGA]G[ACG][AG][AG][TAC][GT][AT][AGC][GTA][GTC]G[TA]G[AG]A -------------------------------------------------------------------------------- Time 15.73 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 16 llr = 216 E-value = 1.6e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 111:14313::1:12::::4 pos.-specific C 163493571931923a3:85 probability G :3:1:::31::::21:4:31 matrix T 8164:33:5189165:3a:: bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * * * Relative 1.2 * **** * ** Entropy 1.0 * * * **** * ** (19.5 bits) 0.8 * * * * **** * *** 0.6 ***** * **** * *** 0.4 ******** ***** ***** 0.2 ******************** 0.0 -------------------- Multilevel TCTCCACCTCTTCTTCGTCC consensus GCT CAGA C C C GA sequence TT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 33968 473 3.35e-10 TCAAACTTCC TCTCCCCCTCCTCTTCCTCC TTTCTCCC 27414 376 4.61e-09 ACGGCACGCA TGCCCACGTCTTCTTCTTCC ACACGCGGAA 6370 147 1.06e-08 ACTTGTGAAT TGTTCACATCTTCTTCGTCA GAGTTACGCT 11841 373 3.18e-08 ACTTCCCCCC TCCTCCACCCTTCCTCGTCA AAGCCTCTCT 22197 462 9.27e-08 TCACATCGTC TCTTCCTCACCTCCACCTCA ACACGAAAGT 269297 201 1.02e-07 ATCACTCCCT CGCTCTCCTCTTCGCCGTCC TCCCACCCCA 23657 161 1.37e-07 GACATCCAAA TCTCCATGGCTTCCTCTTCC GTCAGCTCGT 5394 6 1.99e-07 CACTT TCACCACCACCTCGCCCTCC ACGAGATGTG 25478 474 1.99e-07 TTTTGTTCAC TCCTCTACTCTTCTGCTTGC ATTTACA 42660 367 2.17e-07 AGGCAGGCGG AGTGCACCTCTTCTTCGTGA CGTGTCGGAT 21623 336 2.38e-07 GTTGTTCCCA TCTTCCTCACCTCACCCTCA CACAACCTTC 11842 383 9.32e-07 CAATGGTAAT TCTTCACCATTCCTACGTGA AAATAGTGTC 262125 361 1.63e-06 CATAGCAAAC CACCACACTCTTCTTCCTCC TGCTTCGAGC 39516 2 1.86e-06 C TCTGCTCGCTTTCTTCGTCG TATCATAGGG 21143 419 2.71e-06 CAAACATACA TTTCCTTCACTTTGACGTCA ACAAGAAACG 269274 315 4.32e-06 CATTAACCTC TGTCAAAGTCTACTCCTTGC TTCGAGAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33968 3.4e-10 472_[+3]_8 27414 4.6e-09 375_[+3]_105 6370 1.1e-08 146_[+3]_334 11841 3.2e-08 372_[+3]_108 22197 9.3e-08 461_[+3]_19 269297 1e-07 200_[+3]_280 23657 1.4e-07 160_[+3]_320 5394 2e-07 5_[+3]_475 25478 2e-07 473_[+3]_7 42660 2.2e-07 366_[+3]_114 21623 2.4e-07 335_[+3]_145 11842 9.3e-07 382_[+3]_98 262125 1.6e-06 360_[+3]_120 39516 1.9e-06 1_[+3]_479 21143 2.7e-06 418_[+3]_62 269274 4.3e-06 314_[+3]_166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=16 33968 ( 473) TCTCCCCCTCCTCTTCCTCC 1 27414 ( 376) TGCCCACGTCTTCTTCTTCC 1 6370 ( 147) TGTTCACATCTTCTTCGTCA 1 11841 ( 373) TCCTCCACCCTTCCTCGTCA 1 22197 ( 462) TCTTCCTCACCTCCACCTCA 1 269297 ( 201) CGCTCTCCTCTTCGCCGTCC 1 23657 ( 161) TCTCCATGGCTTCCTCTTCC 1 5394 ( 6) TCACCACCACCTCGCCCTCC 1 25478 ( 474) TCCTCTACTCTTCTGCTTGC 1 42660 ( 367) AGTGCACCTCTTCTTCGTGA 1 21623 ( 336) TCTTCCTCACCTCACCCTCA 1 11842 ( 383) TCTTCACCATTCCTACGTGA 1 262125 ( 361) CACCACACTCTTCTTCCTCC 1 39516 ( 2) TCTGCTCGCTTTCTTCGTCG 1 21143 ( 419) TTTCCTTCACTTTGACGTCA 1 269274 ( 315) TGTCAAAGTCTACTCCTTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14430 bayes= 10.5528 E= 1.6e-006 -207 -93 -1064 163 -207 124 40 -206 -207 39 -1064 126 -1064 88 -92 74 -107 188 -1064 -1064 73 39 -1064 -7 -7 107 -1064 -7 -207 153 8 -1064 25 -93 -192 93 -1064 188 -1064 -106 -1064 7 -1064 152 -207 -193 -1064 174 -1064 198 -1064 -206 -207 -34 -34 110 -49 7 -192 93 -1064 207 -1064 -1064 -1064 39 88 -7 -1064 -1064 -1064 193 -1064 166 8 -1064 73 107 -192 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 16 E= 1.6e-006 0.062500 0.125000 0.000000 0.812500 0.062500 0.562500 0.312500 0.062500 0.062500 0.312500 0.000000 0.625000 0.000000 0.437500 0.125000 0.437500 0.125000 0.875000 0.000000 0.000000 0.437500 0.312500 0.000000 0.250000 0.250000 0.500000 0.000000 0.250000 0.062500 0.687500 0.250000 0.000000 0.312500 0.125000 0.062500 0.500000 0.000000 0.875000 0.000000 0.125000 0.000000 0.250000 0.000000 0.750000 0.062500 0.062500 0.000000 0.875000 0.000000 0.937500 0.000000 0.062500 0.062500 0.187500 0.187500 0.562500 0.187500 0.250000 0.062500 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.312500 0.437500 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.437500 0.500000 0.062500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CG][TC][CT]C[ACT][CAT][CG][TA]C[TC]TCT[TC]C[GCT]T[CG][CA] -------------------------------------------------------------------------------- Time 23.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11841 5.72e-04 372_[+3(3.18e-08)]_108 11842 1.18e-06 16_[+2(1.01e-06)]_173_\ [+1(5.65e-05)]_160_[+3(9.32e-07)]_98 1440 4.75e-07 43_[+1(4.22e-05)]_147_\ [+1(5.65e-05)]_35_[+2(4.14e-06)]_109_[+3(5.06e-07)]_101 17623 9.93e-03 231_[+2(9.11e-06)]_248 17687 6.33e-01 500 20827 3.45e-05 173_[+2(1.93e-05)]_51_\ [+3(8.10e-05)]_89_[+1(1.53e-06)]_134 20829 7.53e-05 289_[+2(7.66e-09)]_190 21143 2.21e-08 [+2(5.84e-07)]_42_[+2(2.79e-05)]_87_\ [+2(8.57e-05)]_188_[+1(4.17e-07)]_26_[+3(2.71e-06)]_17_[+3(6.69e-05)]_25 21623 1.69e-04 335_[+3(2.38e-07)]_145 22197 4.25e-07 85_[+2(5.31e-06)]_145_\ [+1(3.46e-05)]_198_[+3(9.27e-08)]_19 22198 2.86e-05 58_[+2(1.01e-06)]_307_\ [+1(8.68e-05)]_24_[+1(1.98e-06)]_66 22720 1.27e-04 94_[+2(6.54e-07)]_307_\ [+1(1.06e-05)]_66 23657 5.04e-09 106_[+3(1.41e-05)]_34_\ [+3(1.37e-07)]_42_[+2(9.11e-06)]_130_[+1(1.06e-07)]_115 24172 2.56e-05 130_[+1(5.97e-06)]_125_\ [+2(9.08e-07)]_149_[+1(3.52e-06)]_51 24341 6.72e-03 172_[+2(1.30e-05)]_74_\ [+1(8.68e-05)]_221 25299 3.48e-06 373_[+1(7.98e-06)]_20_\ [+2(7.20e-08)]_74 25478 2.49e-08 257_[+2(9.11e-06)]_120_\ [+1(4.17e-07)]_63_[+3(1.99e-07)]_7 262125 1.39e-03 199_[+1(6.89e-05)]_149_\ [+3(1.63e-06)]_120 269274 1.05e-08 314_[+3(4.32e-06)]_5_[+2(1.15e-08)]_\ 55_[+1(5.97e-06)]_73 269297 2.45e-05 167_[+1(7.98e-06)]_21_\ [+3(1.02e-07)]_280 26941 1.44e-05 [+2(5.84e-07)]_63_[+1(1.98e-06)]_\ 404 27414 3.52e-10 192_[+2(3.23e-07)]_52_\ [+1(5.04e-06)]_98_[+3(4.61e-09)]_105 3393 8.61e-05 77_[+1(3.19e-05)]_186_\ [+2(8.15e-07)]_204 33968 1.15e-07 388_[+2(7.85e-06)]_63_\ [+3(3.35e-10)]_8 37980 6.22e-05 367_[+2(4.64e-07)]_49_\ [+1(1.41e-05)]_51 39516 4.33e-07 1_[+3(1.86e-06)]_55_[+2(7.85e-06)]_\ 183_[+1(1.19e-06)]_47_[+3(9.80e-05)]_141 4067 7.98e-02 282_[+2(1.21e-05)]_197 42660 2.44e-08 112_[+2(1.94e-07)]_100_\ [+1(1.75e-05)]_121_[+3(2.17e-07)]_114 5394 1.99e-07 5_[+3(1.99e-07)]_79_[+2(5.62e-05)]_\ 121_[+1(6.96e-06)]_15_[+2(5.31e-06)]_206 6370 1.00e-05 146_[+3(1.06e-08)]_179_\ [+1(4.04e-05)]_143 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************