******************************************************************************** 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/133/133.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42459 1.0000 500 4761 1.0000 500 43134 1.0000 500 13154 1.0000 500 8155 1.0000 500 47586 1.0000 500 38651 1.0000 500 48262 1.0000 500 43352 1.0000 500 49102 1.0000 500 49671 1.0000 500 49924 1.0000 500 50210 1.0000 500 34071 1.0000 500 45547 1.0000 500 45750 1.0000 500 6839 1.0000 500 42515 1.0000 500 48606 1.0000 500 44214 1.0000 500 46933 1.0000 500 54026 1.0000 500 41555 1.0000 500 43335 1.0000 500 47200 1.0000 500 43269 1.0000 500 36547 1.0000 500 34340 1.0000 500 49141 1.0000 500 45644 1.0000 500 37257 1.0000 500 49911 1.0000 500 46060 1.0000 500 49815 1.0000 500 45978 1.0000 500 45242 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/133/133.seqs.fa -oc motifs/133 -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= 36 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= 18000 N= 36 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.230 G 0.220 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.230 G 0.220 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 23 llr = 235 E-value = 1.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 9:::9162:186 pos.-specific C :6:9:9:::92: probability G :1:11::7:::3 matrix T :3a:::4:a::: bits 2.2 2.0 1.7 1.5 **** * Relative 1.3 * **** *** Entropy 1.1 * **** **** (14.8 bits) 0.9 * ********* 0.7 * ********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACTCACAGTCAA consensus T TA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 49671 441 7.40e-08 AATTGAAGAG ACTCACAGTCAA GCGTTGCCTT 38651 78 1.33e-07 CCGTAGACTA ACTCACAGTCAG CCCAAAGTCA 54026 473 6.44e-07 TCGCCCTTTC ATTCACTGTCAA CGAGAATTGA 49924 98 6.44e-07 AGGCAGTCAC AGTCACAGTCAA ATCGGATTTG 43134 440 1.21e-06 GTCAAGATCT ACTCACTATCAA CATCTTTCTG 46933 466 1.40e-06 AAAATTTTTT ACTCAAAGTCAA CACATACATC 49815 23 3.31e-06 CCGTTAAGTG ACTCACAATCCA ATACACTTCT 49102 310 3.31e-06 ATTTCGATGT GCTCACAGTCAA ACTCACCGGT 45242 284 3.99e-06 CGGCCCTCAC ATTCACTGTCCG TTTCACTTCC 46060 218 5.06e-06 ACTCGTCAAT CCTCACAGTCAG GACAAAACCA 47200 197 5.06e-06 TTGATATGAA AATCACTGTCAA CAGCATGAGC 43269 163 5.93e-06 GTTTTTATAT ATTCGCAGTCAG CGTCAAGGGT 48262 216 8.45e-06 GCTGTCACAT AGTCACAGTCAC TTACCAGTGA 37257 105 1.02e-05 CAATGGCGGT ACTAACTGTCAG AGTCCTCTGG 34071 334 1.09e-05 ATTGGTCTTC ACTGACAATCAG CAGTGAAAGG 43352 433 1.09e-05 TCACATTCAC ATTCACATTCAA CTAGTACACT 45750 248 1.46e-05 TTTGTTTACC ACTCACTGTCCT AACAGCGATC 48606 275 2.02e-05 TGATGAAAGG ATTCAAAATCAG TTATGAAGTC 43335 119 2.34e-05 GGAAAATGGG ATTCGCTGTCCA AGTCGAAGCT 42459 223 3.13e-05 TTTCTAACGG ACTCAATGTAAG CGACATCCTC 4761 420 3.80e-05 CGAGGGTCGC ACTCACAGAAAA CGAATTGTTT 36547 382 4.09e-05 CGGTTGCTGA ACTGACTGTGAA ATCCAACGAG 42515 185 5.03e-05 TTGGTTATCT AGACACAATCAA ATGAAATTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49671 7.4e-08 440_[+1]_48 38651 1.3e-07 77_[+1]_411 54026 6.4e-07 472_[+1]_16 49924 6.4e-07 97_[+1]_391 43134 1.2e-06 439_[+1]_49 46933 1.4e-06 465_[+1]_23 49815 3.3e-06 22_[+1]_466 49102 3.3e-06 309_[+1]_179 45242 4e-06 283_[+1]_205 46060 5.1e-06 217_[+1]_271 47200 5.1e-06 196_[+1]_292 43269 5.9e-06 162_[+1]_326 48262 8.4e-06 215_[+1]_273 37257 1e-05 104_[+1]_384 34071 1.1e-05 333_[+1]_155 43352 1.1e-05 432_[+1]_56 45750 1.5e-05 247_[+1]_241 48606 2e-05 274_[+1]_214 43335 2.3e-05 118_[+1]_370 42459 3.1e-05 222_[+1]_266 4761 3.8e-05 419_[+1]_69 36547 4.1e-05 381_[+1]_107 42515 5e-05 184_[+1]_304 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=23 49671 ( 441) ACTCACAGTCAA 1 38651 ( 78) ACTCACAGTCAG 1 54026 ( 473) ATTCACTGTCAA 1 49924 ( 98) AGTCACAGTCAA 1 43134 ( 440) ACTCACTATCAA 1 46933 ( 466) ACTCAAAGTCAA 1 49815 ( 23) ACTCACAATCCA 1 49102 ( 310) GCTCACAGTCAA 1 45242 ( 284) ATTCACTGTCCG 1 46060 ( 218) CCTCACAGTCAG 1 47200 ( 197) AATCACTGTCAA 1 43269 ( 163) ATTCGCAGTCAG 1 48262 ( 216) AGTCACAGTCAC 1 37257 ( 105) ACTAACTGTCAG 1 34071 ( 334) ACTGACAATCAG 1 43352 ( 433) ATTCACATTCAA 1 45750 ( 248) ACTCACTGTCCT 1 48606 ( 275) ATTCAAAATCAG 1 43335 ( 119) ATTCGCTGTCCA 1 42459 ( 223) ACTCAATGTAAG 1 4761 ( 420) ACTCACAGAAAA 1 36547 ( 382) ACTGACTGTGAA 1 42515 ( 185) AGACACAATCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17604 bayes= 10.6433 E= 1.4e-007 173 -240 -233 -1117 -266 129 -75 -7 -266 -1117 -1117 180 -266 192 -134 -1117 173 -1117 -134 -1117 -108 192 -1117 -1117 114 -1117 -1117 51 -34 -1117 175 -265 -266 -1117 -1117 180 -166 192 -233 -1117 158 -41 -1117 -1117 104 -240 66 -265 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 23 E= 1.4e-007 0.913043 0.043478 0.043478 0.000000 0.043478 0.565217 0.130435 0.260870 0.043478 0.000000 0.000000 0.956522 0.043478 0.869565 0.086957 0.000000 0.913043 0.000000 0.086957 0.000000 0.130435 0.869565 0.000000 0.000000 0.608696 0.000000 0.000000 0.391304 0.217391 0.000000 0.739130 0.043478 0.043478 0.000000 0.000000 0.956522 0.086957 0.869565 0.043478 0.000000 0.826087 0.173913 0.000000 0.000000 0.565217 0.043478 0.347826 0.043478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[CT]TCAC[AT][GA]TCA[AG] -------------------------------------------------------------------------------- Time 12.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 23 llr = 251 E-value = 7.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :31:312:22114327a352: pos.-specific C 82223414336:572:::12: probability G :271:2::2:37::62:3:2a matrix T 23:7537635:2:::1:344: bits 2.2 * 2.0 * 1.7 * * 1.5 * * Relative 1.3 * * * Entropy 1.1 * * * * (15.8 bits) 0.9 * ** ** *** ** * 0.7 * ** ** ******* * * 0.4 * *** ** ********** * 0.2 * ****** ********** * 0.0 --------------------- Multilevel CAGTTCTTCTCGCCGAAAATG consensus TTC AT CTCG AAA GTG sequence C G C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 34340 381 4.68e-09 TCGACGAAAA CAGTCCTTCACGACGAATTTG GCTAACTTTT 38651 39 3.20e-08 TCGGAAAATG CGGTCTTCTCGGACGAATTTG GCATGCAACC 45547 394 5.31e-08 AACTACGCCT CACTTCTCTCCGCCGAAACTG TGTGACTGTG 49141 107 2.73e-07 CTTAAGTGTT CTCTACACCTCGACGAATAGG AAATCTAACG 46060 385 6.73e-07 ACTTTGCCAA CTATTCTTATCGAAGGAGTTG GGTCGACGCA 42515 411 1.35e-06 GACAGTAGCT CCCTCTTTACGGAAGAAGAGG AGCCTGCTGT 48606 197 1.51e-06 TCATCATATC CTCTCCTTCCCGATGAAAAGG GCATATGATA 48262 460 1.51e-06 CTTTTTTTCG CTCTAGTTTCGGCAAAAGATG TACCTGCAAA 34071 20 3.46e-06 CTTTTACCAG CCGTTCACGTCGCAATAGATG AGGTACATGG 42459 416 3.46e-06 CGAAAGAAAC CCGCTGTTGTCACAGAATTGG TGTTTTAAGT 43269 359 4.61e-06 AAGTCCGATT TCGGTATTTTGGCCGAAGTCG ATGTTGGCGT 47200 33 4.61e-06 ACAAGGACTT CGATTCTTCACGACAGAGTCG CATAGCGTTA 44214 10 5.06e-06 GCTAAACTC CAATTGTTTTCGTCCAATTTG GAAGAAGCTC 46933 224 5.55e-06 GACGAATATT CAGGTTTCAACGCACAAAAAG TCCCCTTGCG 49102 430 6.07e-06 ATTAAAAGGA TAGCTTTCGTCGACAGAGTCG GCAAATTAGC 49815 298 6.63e-06 CGTCCGTTTT TGGTACCCATGGCCGAAAAAG CTAGATATTT 50210 285 6.63e-06 AAATACGGTT CAGTACTTTAGTACCAAACTG CGCGTACAAC 47586 170 6.63e-06 ATAAAGATAC CAGTATATGTAACCGAATTTG GAACGTTTCG 43352 197 7.24e-06 GAGAAACAGT CTGGTCTTCCATCAGAATTGG AGAAAAGAAC 49924 215 8.59e-06 CGCAAGTGAC TTGTCTTCTCGACCCAAAACG GGAAGCACGG 43335 14 1.62e-05 CAATCACAGG CGGCCATCCCCTCCGTAAATG GTCGCGATTG 49911 438 3.69e-05 AGGCGGTGTG CAGCATACCTCTACAGAAAAG TCTCATATTT 45750 460 3.69e-05 AATGGAATAT TTGTTGCTGTTGCCCAAGAAG GAAGTGACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34340 4.7e-09 380_[+2]_99 38651 3.2e-08 38_[+2]_441 45547 5.3e-08 393_[+2]_86 49141 2.7e-07 106_[+2]_373 46060 6.7e-07 384_[+2]_95 42515 1.4e-06 410_[+2]_69 48606 1.5e-06 196_[+2]_283 48262 1.5e-06 459_[+2]_20 34071 3.5e-06 19_[+2]_460 42459 3.5e-06 415_[+2]_64 43269 4.6e-06 358_[+2]_121 47200 4.6e-06 32_[+2]_447 44214 5.1e-06 9_[+2]_470 46933 5.5e-06 223_[+2]_256 49102 6.1e-06 429_[+2]_50 49815 6.6e-06 297_[+2]_182 50210 6.6e-06 284_[+2]_195 47586 6.6e-06 169_[+2]_310 43352 7.2e-06 196_[+2]_283 49924 8.6e-06 214_[+2]_265 43335 1.6e-05 13_[+2]_466 49911 3.7e-05 437_[+2]_42 45750 3.7e-05 459_[+2]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=23 34340 ( 381) CAGTCCTTCACGACGAATTTG 1 38651 ( 39) CGGTCTTCTCGGACGAATTTG 1 45547 ( 394) CACTTCTCTCCGCCGAAACTG 1 49141 ( 107) CTCTACACCTCGACGAATAGG 1 46060 ( 385) CTATTCTTATCGAAGGAGTTG 1 42515 ( 411) CCCTCTTTACGGAAGAAGAGG 1 48606 ( 197) CTCTCCTTCCCGATGAAAAGG 1 48262 ( 460) CTCTAGTTTCGGCAAAAGATG 1 34071 ( 20) CCGTTCACGTCGCAATAGATG 1 42459 ( 416) CCGCTGTTGTCACAGAATTGG 1 43269 ( 359) TCGGTATTTTGGCCGAAGTCG 1 47200 ( 33) CGATTCTTCACGACAGAGTCG 1 44214 ( 10) CAATTGTTTTCGTCCAATTTG 1 46933 ( 224) CAGGTTTCAACGCACAAAAAG 1 49102 ( 430) TAGCTTTCGTCGACAGAGTCG 1 49815 ( 298) TGGTACCCATGGCCGAAAAAG 1 50210 ( 285) CAGTACTTTAGTACCAAACTG 1 47586 ( 170) CAGTATATGTAACCGAATTTG 1 43352 ( 197) CTGGTCTTCCATCAGAATTGG 1 49924 ( 215) TTGTCTTCTCGACCCAAAACG 1 43335 ( 14) CGGCCATCCCCTCCGTAAATG 1 49911 ( 438) CAGCATACCTCTACAGAAAAG 1 45750 ( 460) TTGTTGCTGTTGCCCAAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17280 bayes= 9.95435 E= 7.7e+002 -1117 176 -1117 -33 34 -41 -34 15 -108 -8 157 -1117 -1117 -41 -75 134 -8 18 -1117 80 -166 92 -34 15 -66 -141 -1117 143 -1117 92 -1117 104 -66 40 -1 15 -66 59 -1117 80 -166 129 47 -265 -108 -1117 166 -66 66 118 -1117 -265 14 150 -1117 -265 -34 -8 136 -1117 142 -1117 -34 -166 186 -1117 -1117 -1117 34 -1117 66 15 79 -141 -1117 66 -66 -41 -1 66 -1117 -1117 219 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 23 E= 7.7e+002 0.000000 0.782609 0.000000 0.217391 0.347826 0.173913 0.173913 0.304348 0.130435 0.217391 0.652174 0.000000 0.000000 0.173913 0.130435 0.695652 0.260870 0.260870 0.000000 0.478261 0.086957 0.434783 0.173913 0.304348 0.173913 0.086957 0.000000 0.739130 0.000000 0.434783 0.000000 0.565217 0.173913 0.304348 0.217391 0.304348 0.173913 0.347826 0.000000 0.478261 0.086957 0.565217 0.304348 0.043478 0.130435 0.000000 0.695652 0.173913 0.434783 0.521739 0.000000 0.043478 0.304348 0.652174 0.000000 0.043478 0.217391 0.217391 0.565217 0.000000 0.739130 0.000000 0.173913 0.086957 1.000000 0.000000 0.000000 0.000000 0.347826 0.000000 0.347826 0.304348 0.478261 0.086957 0.000000 0.434783 0.173913 0.173913 0.217391 0.434783 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][AT][GC]T[TAC][CT]T[TC][CTG][TC][CG]G[CA][CA][GAC]AA[AGT][AT][TG]G -------------------------------------------------------------------------------- Time 26.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 13 llr = 158 E-value = 7.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::545a6a48276 pos.-specific C :7:9254:::::822 probability G ::::2:2:4:52::2 matrix T a3a112::::1::2: bits 2.2 2.0 * * 1.7 * ** * * 1.5 * ** * * * Relative 1.3 * ** * * ** Entropy 1.1 **** *** ** (17.5 bits) 0.9 **** *** ** 0.7 **** ********* 0.4 **** ********** 0.2 *************** 0.0 --------------- Multilevel TCTCACAAAAGACAA consensus T CAC G A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 48262 299 1.21e-08 CAGGAGATGC TCTCACAAAAAACAA AAATTCCTCC 46060 171 8.23e-08 GAATCACTCT TCTCACAAGAGACAG TCAACTTCCG 49102 386 1.42e-07 CTCTCGGGAG TCTCACCAGAGGCAA CCCAGCAAGC 13154 232 3.64e-07 GTTTTCCATC TTTCACAAAAAACAC CACAATTCCA 49815 421 4.10e-07 GGTCTCGAAA TCTCACCAAAAAAAA TTTGTGAGGT 43335 271 4.10e-07 TGACCAAGCA TCTCGCCAAAGACCA GCAGATCTAT 4761 384 5.78e-07 TCACTGCAAC TCTCCAGAGAAACAA ATGGGTCTTC 47200 245 1.63e-06 CTCAATATAA TTTCTAAAGAGACAA CACATTTAAA 45242 371 3.25e-06 ACACGTCATA TTTCCAGAAAGGCAA ACGGAAACAC 36547 310 4.25e-06 TTTGAATACC TTTCGAAAAAGACTC ATTCGAGAGT 42459 349 5.43e-06 TTGGAAAGCT TCTCATAAAAAAACA CGGAATCGCT 47586 481 5.75e-06 TCATACATAA TCTCAACAAATACTG CAACC 41555 447 7.96e-06 CATATGACGA TCTTCTCAGAGACAC AGTACGTCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48262 1.2e-08 298_[+3]_187 46060 8.2e-08 170_[+3]_315 49102 1.4e-07 385_[+3]_100 13154 3.6e-07 231_[+3]_254 49815 4.1e-07 420_[+3]_65 43335 4.1e-07 270_[+3]_215 4761 5.8e-07 383_[+3]_102 47200 1.6e-06 244_[+3]_241 45242 3.2e-06 370_[+3]_115 36547 4.3e-06 309_[+3]_176 42459 5.4e-06 348_[+3]_137 47586 5.8e-06 480_[+3]_5 41555 8e-06 446_[+3]_39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=13 48262 ( 299) TCTCACAAAAAACAA 1 46060 ( 171) TCTCACAAGAGACAG 1 49102 ( 386) TCTCACCAGAGGCAA 1 13154 ( 232) TTTCACAAAAAACAC 1 49815 ( 421) TCTCACCAAAAAAAA 1 43335 ( 271) TCTCGCCAAAGACCA 1 4761 ( 384) TCTCCAGAGAAACAA 1 47200 ( 245) TTTCTAAAGAGACAA 1 45242 ( 371) TTTCCAGAAAGGCAA 1 36547 ( 310) TTTCGAAAAAGACTC 1 42459 ( 349) TCTCATAAAAAAACA 1 47586 ( 481) TCTCAACAAATACTG 1 41555 ( 447) TCTTCTCAGAGACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 17496 bayes= 10.1486 E= 7.1e+001 -1035 -1035 -1035 187 -1035 159 -1035 17 -1035 -1035 -1035 187 -1035 200 -1035 -183 97 0 -51 -183 48 100 -1035 -83 74 74 -51 -1035 186 -1035 -1035 -1035 116 -1035 81 -1035 186 -1035 -1035 -1035 48 -1035 129 -183 162 -1035 -51 -1035 -84 188 -1035 -1035 133 -58 -1035 -83 116 0 -51 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 13 E= 7.1e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.692308 0.000000 0.307692 0.000000 0.000000 0.000000 1.000000 0.000000 0.923077 0.000000 0.076923 0.538462 0.230769 0.153846 0.076923 0.384615 0.461538 0.000000 0.153846 0.461538 0.384615 0.153846 0.000000 1.000000 0.000000 0.000000 0.000000 0.615385 0.000000 0.384615 0.000000 1.000000 0.000000 0.000000 0.000000 0.384615 0.000000 0.538462 0.076923 0.846154 0.000000 0.153846 0.000000 0.153846 0.846154 0.000000 0.000000 0.692308 0.153846 0.000000 0.153846 0.615385 0.230769 0.153846 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CT]TC[AC][CA][AC]A[AG]A[GA]ACA[AC] -------------------------------------------------------------------------------- Time 39.50 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42459 1.02e-05 222_[+1(3.13e-05)]_114_\ [+3(5.43e-06)]_52_[+2(3.46e-06)]_49_[+3(3.45e-05)] 4761 2.71e-04 383_[+3(5.78e-07)]_21_\ [+1(3.80e-05)]_69 43134 1.21e-02 136_[+1(8.90e-05)]_169_\ [+1(6.95e-05)]_110_[+1(1.21e-06)]_49 13154 4.32e-03 231_[+3(3.64e-07)]_254 8155 6.27e-01 500 47586 4.74e-04 169_[+2(6.63e-06)]_290_\ [+3(5.75e-06)]_5 38651 6.62e-08 38_[+2(3.20e-08)]_18_[+1(1.33e-07)]_\ 19_[+2(7.31e-05)]_22_[+1(3.56e-05)]_337 48262 5.87e-09 215_[+1(8.45e-06)]_71_\ [+3(1.21e-08)]_146_[+2(1.51e-06)]_20 43352 1.17e-03 196_[+2(7.24e-06)]_203_\ [+1(3.56e-05)]_[+1(1.09e-05)]_56 49102 8.48e-08 309_[+1(3.31e-06)]_64_\ [+3(1.42e-07)]_29_[+2(6.07e-06)]_50 49671 1.45e-03 440_[+1(7.40e-08)]_48 49924 5.70e-05 97_[+1(6.44e-07)]_105_\ [+2(8.59e-06)]_265 50210 2.94e-02 284_[+2(6.63e-06)]_195 34071 7.34e-05 19_[+2(3.46e-06)]_293_\ [+1(1.09e-05)]_155 45547 2.02e-04 393_[+2(5.31e-08)]_86 45750 3.48e-03 247_[+1(1.46e-05)]_200_\ [+2(3.69e-05)]_20 6839 5.16e-01 500 42515 4.25e-04 184_[+1(5.03e-05)]_214_\ [+2(1.35e-06)]_69 48606 4.85e-04 196_[+2(1.51e-06)]_57_\ [+1(2.02e-05)]_214 44214 1.10e-02 9_[+2(5.06e-06)]_470 46933 8.04e-05 223_[+2(5.55e-06)]_221_\ [+1(1.40e-06)]_23 54026 3.91e-03 472_[+1(6.44e-07)]_16 41555 1.13e-02 446_[+3(7.96e-06)]_39 43335 3.13e-06 13_[+2(1.62e-05)]_84_[+1(2.34e-05)]_\ 140_[+3(4.10e-07)]_215 47200 8.93e-07 32_[+2(4.61e-06)]_143_\ [+1(5.06e-06)]_36_[+3(1.63e-06)]_241 43269 2.57e-04 162_[+1(5.93e-06)]_184_\ [+2(4.61e-06)]_121 36547 2.42e-03 309_[+3(4.25e-06)]_57_\ [+1(4.09e-05)]_107 34340 6.23e-05 380_[+2(4.68e-09)]_99 49141 7.39e-04 106_[+2(2.73e-07)]_373 45644 7.34e-01 500 37257 3.81e-02 104_[+1(1.02e-05)]_384 49911 1.43e-01 437_[+2(3.69e-05)]_42 46060 1.01e-08 170_[+3(8.23e-08)]_32_\ [+1(5.06e-06)]_155_[+2(6.73e-07)]_95 49815 2.42e-07 22_[+1(3.31e-06)]_263_\ [+2(6.63e-06)]_102_[+3(4.10e-07)]_65 45978 9.79e-01 500 45242 3.16e-05 283_[+1(3.99e-06)]_54_\ [+3(7.28e-05)]_6_[+3(3.25e-06)]_115 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************