******************************************************************************** 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/150/150.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31474 1.0000 500 42505 1.0000 500 17671 1.0000 500 17948 1.0000 500 46360 1.0000 500 46440 1.0000 500 13119 1.0000 500 12963 1.0000 500 46613 1.0000 500 5396 1.0000 500 21183 1.0000 500 47178 1.0000 500 54805 1.0000 500 48160 1.0000 500 48457 1.0000 500 22459 1.0000 500 48502 1.0000 500 22622 1.0000 500 29967 1.0000 500 6698 1.0000 500 22955 1.0000 500 49985 1.0000 500 44207 1.0000 500 33660 1.0000 500 44335 1.0000 500 34078 1.0000 500 51700 1.0000 500 11441 1.0000 500 44757 1.0000 500 45966 1.0000 500 45969 1.0000 500 46005 1.0000 500 45124 1.0000 500 50464 1.0000 500 54028 1.0000 500 45385 1.0000 500 47403 1.0000 500 48956 1.0000 500 40441 1.0000 500 48823 1.0000 500 49579 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/150/150.seqs.fa -oc motifs/150 -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= 41 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= 20500 N= 41 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.254 G 0.230 T 0.251 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.254 G 0.230 T 0.251 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 30 llr = 282 E-value = 3.6e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :2a:9::2a535 pos.-specific C 13:9:::3:3:: probability G 14:1:a:4:3:4 matrix T 81::1:a1::71 bits 2.1 * 1.9 * 1.7 * ** * 1.5 ** ** * Relative 1.3 ***** * Entropy 1.1 ***** * * (13.6 bits) 0.8 * ***** * * 0.6 * ***** * ** 0.4 * ***** **** 0.2 ************ 0.0 ------------ Multilevel TGACAGTGAATA consensus C C CAG sequence A A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48457 66 1.78e-07 ACGACTTTTT TGACAGTGAGTA GTCGCTACGA 34078 75 5.07e-07 CAAGATTGAT TGACAGTGAGTG CTTCCATAGT 48160 236 7.54e-07 GACATGACAT TGACAGTGAAAA CACTATGGTT 47178 11 7.54e-07 TGACTGACTG TGACAGTGAAAA ATCAATCAAT 12963 216 1.24e-06 ACAAAAGAGA TCACAGTCAATA ACATGTAAAT 13119 216 1.24e-06 ACAAAAGAGT TCACAGTCAATA ACGTGTAAAT 31474 285 3.71e-06 GTACGGGGCC TAACAGTAAATA CACTACCGGT 49985 163 5.38e-06 GTCCTATCTC TAACAGTAAATG GCCATTTGAT 45385 335 6.73e-06 AGACACTAGC TGACTGTGAATA TAGAGGAGAC 17671 210 6.73e-06 TTGTTCCAAC TGACTGTGAATA CGGCTGACAG 44757 269 7.90e-06 TGACGATTTG TTACAGTCAGTA CCTCGCCCTG 45966 442 8.97e-06 CGATCTACAC TAACAGTAACTG TAAATAGCCA 49579 271 9.65e-06 AATGTCAGGG TCACAGTCACAG GCATAATTGC 48823 277 9.65e-06 CACAATACAA TCACAGTCACAG TCACAGTCAG 50464 455 1.10e-05 GCTGCTGCTG TGAGAGTGACTA GTGGGGGAAA 48956 34 1.29e-05 TTGATAACGA GGACAGTGAGAA ATTACATTAA 22459 289 1.29e-05 AGCCCGCACC GAACAGTGACTA ACCAAAGGAT 48502 246 2.29e-05 CTCCATTCGT TTACAGTTAATA TTACACTCCA 46613 42 2.29e-05 ACAAGAATCC TCACAGTCAAAT GACACGCCAC 21183 51 3.50e-05 GGGGTTGTCG CCACAGTCAGTA CGTCACGTCA 54028 250 3.72e-05 TGGACTGTGG TGACGGTGACTG CGTGTCTATG 46005 433 4.07e-05 TGGAGAACAC GAACAGTAACTG TAATTCGTAA 33660 9 4.07e-05 CAGTGGTT TGTCAGTGAGTG AGTGAGTGAG 11441 133 5.18e-05 ACGCCAAGAC GAACAGTAAAAG TGAAGTGTGC 17948 437 6.91e-05 TTTACACCAC TCAGAGTCAATT AGTCTCACTT 44207 323 1.16e-04 TGAATAGTTA TCACAGGAAGTG ACACTACTAG 45969 296 1.23e-04 GAGATCCGAG AAACAGTCACAA CGTACGAAGT 51700 327 1.38e-04 GATAACCGTT TTACAGTTAAAT CTGAGAGCCG 22955 141 1.38e-04 GACAAATTAG TGACTGTGCATG GATCCCATCC 46440 232 1.38e-04 CAACAACAGA CGAGAGTGAGAA ATCCCCCCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48457 1.8e-07 65_[+1]_423 34078 5.1e-07 74_[+1]_414 48160 7.5e-07 235_[+1]_253 47178 7.5e-07 10_[+1]_478 12963 1.2e-06 215_[+1]_273 13119 1.2e-06 215_[+1]_273 31474 3.7e-06 284_[+1]_204 49985 5.4e-06 162_[+1]_326 45385 6.7e-06 334_[+1]_154 17671 6.7e-06 209_[+1]_279 44757 7.9e-06 268_[+1]_220 45966 9e-06 441_[+1]_47 49579 9.7e-06 270_[+1]_218 48823 9.7e-06 276_[+1]_212 50464 1.1e-05 454_[+1]_34 48956 1.3e-05 33_[+1]_455 22459 1.3e-05 288_[+1]_200 48502 2.3e-05 245_[+1]_243 46613 2.3e-05 41_[+1]_447 21183 3.5e-05 50_[+1]_438 54028 3.7e-05 249_[+1]_239 46005 4.1e-05 432_[+1]_56 33660 4.1e-05 8_[+1]_480 11441 5.2e-05 132_[+1]_356 17948 6.9e-05 436_[+1]_52 44207 0.00012 322_[+1]_166 45969 0.00012 295_[+1]_193 51700 0.00014 326_[+1]_162 22955 0.00014 140_[+1]_348 46440 0.00014 231_[+1]_257 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=30 48457 ( 66) TGACAGTGAGTA 1 34078 ( 75) TGACAGTGAGTG 1 48160 ( 236) TGACAGTGAAAA 1 47178 ( 11) TGACAGTGAAAA 1 12963 ( 216) TCACAGTCAATA 1 13119 ( 216) TCACAGTCAATA 1 31474 ( 285) TAACAGTAAATA 1 49985 ( 163) TAACAGTAAATG 1 45385 ( 335) TGACTGTGAATA 1 17671 ( 210) TGACTGTGAATA 1 44757 ( 269) TTACAGTCAGTA 1 45966 ( 442) TAACAGTAACTG 1 49579 ( 271) TCACAGTCACAG 1 48823 ( 277) TCACAGTCACAG 1 50464 ( 455) TGAGAGTGACTA 1 48956 ( 34) GGACAGTGAGAA 1 22459 ( 289) GAACAGTGACTA 1 48502 ( 246) TTACAGTTAATA 1 46613 ( 42) TCACAGTCAAAT 1 21183 ( 51) CCACAGTCAGTA 1 54028 ( 250) TGACGGTGACTG 1 46005 ( 433) GAACAGTAACTG 1 33660 ( 9) TGTCAGTGAGTG 1 11441 ( 133) GAACAGTAAAAG 1 17948 ( 437) TCAGAGTCAATT 1 44207 ( 323) TCACAGGAAGTG 1 45969 ( 296) AAACAGTCACAA 1 51700 ( 327) TTACAGTTAAAT 1 22955 ( 141) TGACTGTGCATG 1 46440 ( 232) CGAGAGTGAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 20049 bayes= 10.0572 E= 3.6e-008 -299 -193 -79 161 -19 7 80 -133 186 -1155 -1155 -291 -1155 183 -120 -1155 171 -1155 -278 -133 -1155 -1155 212 -1155 -1155 -1155 -278 195 -41 24 91 -191 186 -292 -1155 -1155 81 7 21 -1155 33 -1155 -1155 141 101 -1155 67 -133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 30 E= 3.6e-008 0.033333 0.066667 0.133333 0.766667 0.233333 0.266667 0.400000 0.100000 0.966667 0.000000 0.000000 0.033333 0.000000 0.900000 0.100000 0.000000 0.866667 0.000000 0.033333 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.033333 0.966667 0.200000 0.300000 0.433333 0.066667 0.966667 0.033333 0.000000 0.000000 0.466667 0.266667 0.266667 0.000000 0.333333 0.000000 0.000000 0.666667 0.533333 0.000000 0.366667 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GCA]ACAGT[GCA]A[ACG][TA][AG] -------------------------------------------------------------------------------- Time 17.22 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 18 llr = 191 E-value = 2.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::3:::1::2 pos.-specific C ::1::42::11: probability G 41:26331::9: matrix T 6998126999:8 bits 2.1 1.9 1.7 ** * * 1.5 ** **** Relative 1.3 *** ***** Entropy 1.1 **** ***** (15.3 bits) 0.8 ***** ***** 0.6 ***** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTTGCTTTTGT consensus G AGG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 22459 48 5.31e-08 AGAGTTCCAC TTTTGCTTTTGT TAGGGTTGCT 45385 200 1.01e-07 GTACCTTAGT TTTTGGTTTTGT TCTAGTAGCC 45124 270 2.95e-07 ATCCAAGGAT TTTTGTTTTTGT GTAACCGAGT 40441 95 1.00e-06 CATTCACTTG TTTTACGTTTGT TAGTCGTGGC 17671 357 1.36e-06 GCTGCTTTTT GTTTGGCTTTGT TAAATCTGTG 44207 165 2.02e-06 GAAGGAAGAA TTTTGCTTTCGT GCCAAGCGGA 49985 104 2.02e-06 AGAAGCGTCA TTTTGCTTATGT TACTGTGAGC 42505 182 3.64e-06 GGGGCGTTTC GTTTATGTTTGT AGAAAGACTG 48160 448 4.55e-06 GATTCGACGT TTTTGCGTTTCT ACTATCCCTT 49579 239 1.01e-05 GAGCAATCGA TTTTACTGTTGT AAACTAAAAT 12963 386 1.01e-05 GTGATGGTAC GTTTATTTTTGA AACAGTCCGT 13119 386 1.01e-05 GTGATGGTAC GTTTATTTTTGA AACAGTCCGT 44335 104 1.21e-05 TGGTGATGTT TTTGGGTTTTCT CAATTTTTGT 47178 467 1.39e-05 CTCTCTCTAT TTCTGCCTTTGT TGCAATCACG 48823 47 1.84e-05 AGACAACAAT GTTGTGGTTTGT GCGAACGAGA 46440 467 1.84e-05 CATTGCATCC GTTTTGTTTCGT CATTGGGTAC 50464 52 2.35e-05 GGAAAGGGTC GTTGGGGTATGT ATGCATATAT 11441 358 4.31e-05 CTTGCCCCGT TGTTGCCTTTGA CGCTGTCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22459 5.3e-08 47_[+2]_441 45385 1e-07 199_[+2]_289 45124 3e-07 269_[+2]_219 40441 1e-06 94_[+2]_394 17671 1.4e-06 356_[+2]_132 44207 2e-06 164_[+2]_324 49985 2e-06 103_[+2]_385 42505 3.6e-06 181_[+2]_307 48160 4.6e-06 447_[+2]_41 49579 1e-05 238_[+2]_250 12963 1e-05 385_[+2]_103 13119 1e-05 385_[+2]_103 44335 1.2e-05 103_[+2]_385 47178 1.4e-05 466_[+2]_22 48823 1.8e-05 46_[+2]_442 46440 1.8e-05 466_[+2]_22 50464 2.4e-05 51_[+2]_437 11441 4.3e-05 357_[+2]_131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=18 22459 ( 48) TTTTGCTTTTGT 1 45385 ( 200) TTTTGGTTTTGT 1 45124 ( 270) TTTTGTTTTTGT 1 40441 ( 95) TTTTACGTTTGT 1 17671 ( 357) GTTTGGCTTTGT 1 44207 ( 165) TTTTGCTTTCGT 1 49985 ( 104) TTTTGCTTATGT 1 42505 ( 182) GTTTATGTTTGT 1 48160 ( 448) TTTTGCGTTTCT 1 49579 ( 239) TTTTACTGTTGT 1 12963 ( 386) GTTTATTTTTGA 1 13119 ( 386) GTTTATTTTTGA 1 44335 ( 104) TTTGGGTTTTCT 1 47178 ( 467) TTCTGCCTTTGT 1 48823 ( 47) GTTGTGGTTTGT 1 46440 ( 467) GTTTTGTTTCGT 1 50464 ( 52) GTTGGGGTATGT 1 11441 ( 358) TGTTGCCTTTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 20049 bayes= 10.9686 E= 2.8e-002 -1081 -1081 76 128 -1081 -1081 -205 191 -1081 -219 -1081 191 -1081 -1081 -46 173 7 -1081 141 -117 -1081 81 54 -18 -1081 -61 27 115 -1081 -1081 -205 191 -126 -1081 -1081 182 -1081 -119 -1081 182 -1081 -119 195 -1081 -67 -1081 -1081 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 2.8e-002 0.000000 0.000000 0.388889 0.611111 0.000000 0.000000 0.055556 0.944444 0.000000 0.055556 0.000000 0.944444 0.000000 0.000000 0.166667 0.833333 0.277778 0.000000 0.611111 0.111111 0.000000 0.444444 0.333333 0.222222 0.000000 0.166667 0.277778 0.555556 0.000000 0.000000 0.055556 0.944444 0.111111 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.888889 0.000000 0.166667 0.000000 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG]TTT[GA][CGT][TG]TTTGT -------------------------------------------------------------------------------- Time 33.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 18 llr = 228 E-value = 7.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 114:191:24a36:3216312 pos.-specific C 6::48:3a23:239:792:73 probability G :73111::62:31:4::2125 matrix T 3224::6::2:1:121:1711 bits 2.1 1.9 * * 1.7 * * * * 1.5 * * * * * Relative 1.3 ** * * * * Entropy 1.1 ** * * * * (18.3 bits) 0.8 ** ** * * ** * * 0.6 ** ****** * ** ** ** 0.4 ********* * ********* 0.2 ********* *********** 0.0 --------------------- Multilevel CGACCATCGAAAACGCCATCG consensus TTGT C AC GC AA A C sequence T C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 12963 168 4.34e-11 CCTCACACTG CGATCATCGCAGACTCCATCG GCAGAAATCG 13119 168 4.34e-11 CCTCACACTG CGATCATCGCAGACTCCATCG GCAGAAATCG 45966 471 3.64e-09 CCATCTGTTT CGGTCACCGGAGACACCATGG CACCGCATC 48823 385 1.53e-07 GCCACTGACA TTGGCATCGAAGCCGCCATGC AAAATCCAGA 46613 336 2.09e-07 ATTGCCAACA TGTCCACCAAAACCGCCAACA ATCTCTCGTA 11441 18 3.42e-07 TCCGGCCTGT CGATCATCCGAAACACCGTTC ATCGAAAGGT 40441 426 3.76e-07 TACCCATAAT CGGCAACCGTACACACCATGG CGACACCAAC 22955 158 4.54e-07 GCATGGATCC CATCCATCGCATCCTCCGTCG CGGAACCATG 33660 457 4.98e-07 AGGAAGAACT TGTCCATCCAACCCGTCATCA TGACTCACCG 45969 408 7.76e-07 GGTGTCGCGA CGGTGATCGCAAACGACCTCT CATTTCATCA 17948 303 1.28e-06 ACGGCAATGA ATGCCACCGAAACCACCCACG AGGGACTGTG 44335 363 1.50e-06 AACGAACGAA CGACCAACACAAACGCAAACC AACTTTCCAT 54028 205 2.94e-06 CACAGCTGAC TGGTGATCCAACACAACAGCG TTGGCTTGTT 54805 475 2.94e-06 AACGAGGTCT TGTTCACCGTATGCTTCATCG CTTCC 46360 370 2.94e-06 GCGTCCCGTT CGACCATCGAAGATGACCAAC CGCAAAGTAG 46005 395 5.08e-06 CTGTTCACAG TAATCAACAAACACGACAACA TCATCATTGG 47403 380 5.42e-06 CAGCAGCACT CTACCGCCGGAAACACCGTTC GCAACAGATA 44207 457 6.16e-06 AGTACGCATT CTAGCATCATAGCTGCCTTCG TACAAGCATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12963 4.3e-11 167_[+3]_312 13119 4.3e-11 167_[+3]_312 45966 3.6e-09 470_[+3]_9 48823 1.5e-07 384_[+3]_95 46613 2.1e-07 335_[+3]_144 11441 3.4e-07 17_[+3]_462 40441 3.8e-07 425_[+3]_54 22955 4.5e-07 157_[+3]_322 33660 5e-07 456_[+3]_23 45969 7.8e-07 407_[+3]_72 17948 1.3e-06 302_[+3]_177 44335 1.5e-06 362_[+3]_117 54028 2.9e-06 204_[+3]_275 54805 2.9e-06 474_[+3]_5 46360 2.9e-06 369_[+3]_110 46005 5.1e-06 394_[+3]_85 47403 5.4e-06 379_[+3]_100 44207 6.2e-06 456_[+3]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=18 12963 ( 168) CGATCATCGCAGACTCCATCG 1 13119 ( 168) CGATCATCGCAGACTCCATCG 1 45966 ( 471) CGGTCACCGGAGACACCATGG 1 48823 ( 385) TTGGCATCGAAGCCGCCATGC 1 46613 ( 336) TGTCCACCAAAACCGCCAACA 1 11441 ( 18) CGATCATCCGAAACACCGTTC 1 40441 ( 426) CGGCAACCGTACACACCATGG 1 22955 ( 158) CATCCATCGCATCCTCCGTCG 1 33660 ( 457) TGTCCATCCAACCCGTCATCA 1 45969 ( 408) CGGTGATCGCAAACGACCTCT 1 17948 ( 303) ATGCCACCGAAACCACCCACG 1 44335 ( 363) CGACCAACACAAACGCAAACC 1 54028 ( 205) TGGTGATCCAACACAACAGCG 1 54805 ( 475) TGTTCACCGTATGCTTCATCG 1 46360 ( 370) CGACCATCGAAGATGACCAAC 1 46005 ( 395) TAATCAACAAACACGACAACA 1 47403 ( 380) CTACCGCCGGAAACACCGTTC 1 44207 ( 457) CTAGCATCATAGCTGCCTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19680 bayes= 10.9418 E= 7.6e-001 -225 127 -1081 41 -126 -1081 154 -18 74 -1081 54 -18 -1081 81 -105 82 -225 172 -105 -1081 183 -1081 -205 -1081 -126 39 -1081 115 -1081 198 -1081 -1081 -26 -61 141 -1081 55 13 -46 -59 191 -1081 -1081 -1081 33 -19 54 -117 120 39 -205 -1081 -1081 181 -1081 -117 33 -1081 95 -18 -26 139 -1081 -117 -225 190 -1081 -1081 120 -61 -46 -217 7 -1081 -205 141 -225 139 -46 -117 -67 13 112 -217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 7.6e-001 0.055556 0.611111 0.000000 0.333333 0.111111 0.000000 0.666667 0.222222 0.444444 0.000000 0.333333 0.222222 0.000000 0.444444 0.111111 0.444444 0.055556 0.833333 0.111111 0.000000 0.944444 0.000000 0.055556 0.000000 0.111111 0.333333 0.000000 0.555556 0.000000 1.000000 0.000000 0.000000 0.222222 0.166667 0.611111 0.000000 0.388889 0.277778 0.166667 0.166667 1.000000 0.000000 0.000000 0.000000 0.333333 0.222222 0.333333 0.111111 0.611111 0.333333 0.055556 0.000000 0.000000 0.888889 0.000000 0.111111 0.333333 0.000000 0.444444 0.222222 0.222222 0.666667 0.000000 0.111111 0.055556 0.944444 0.000000 0.000000 0.611111 0.166667 0.166667 0.055556 0.277778 0.000000 0.055556 0.666667 0.055556 0.666667 0.166667 0.111111 0.166667 0.277778 0.500000 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][GT][AGT][CT]CA[TC]C[GA][AC]A[AGC][AC]C[GAT][CA]CA[TA]C[GC] -------------------------------------------------------------------------------- Time 50.91 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31474 1.54e-02 284_[+1(3.71e-06)]_204 42505 2.08e-02 181_[+2(3.64e-06)]_307 17671 3.85e-05 48_[+2(7.10e-05)]_149_\ [+1(6.73e-06)]_135_[+2(1.36e-06)]_132 17948 6.97e-04 302_[+3(1.28e-06)]_113_\ [+1(6.91e-05)]_52 46360 8.22e-03 369_[+3(2.94e-06)]_110 46440 3.72e-03 466_[+2(1.84e-05)]_22 13119 3.07e-11 167_[+3(4.34e-11)]_27_\ [+1(1.24e-06)]_158_[+2(1.01e-05)]_103 12963 3.07e-11 167_[+3(4.34e-11)]_27_\ [+1(1.24e-06)]_158_[+2(1.01e-05)]_103 46613 1.20e-04 41_[+1(2.29e-05)]_282_\ [+3(2.09e-07)]_144 5396 2.14e-01 421_[+2(7.84e-05)]_67 21183 4.69e-02 50_[+1(3.50e-05)]_438 47178 1.26e-04 10_[+1(7.54e-07)]_444_\ [+2(1.39e-05)]_22 54805 2.07e-02 474_[+3(2.94e-06)]_5 48160 7.12e-05 235_[+1(7.54e-07)]_200_\ [+2(4.55e-06)]_41 48457 1.98e-03 65_[+1(1.78e-07)]_300_\ [+1(1.19e-05)]_111 22459 9.72e-06 47_[+2(5.31e-08)]_229_\ [+1(1.29e-05)]_200 48502 2.99e-02 245_[+1(2.29e-05)]_243 22622 4.83e-01 500 29967 1.78e-01 500 6698 8.54e-01 500 22955 2.47e-04 157_[+3(4.54e-07)]_322 49985 1.05e-04 103_[+2(2.02e-06)]_47_\ [+1(5.38e-06)]_326 44207 2.23e-05 164_[+2(2.02e-06)]_280_\ [+3(6.16e-06)]_23 33660 4.22e-05 8_[+1(4.07e-05)]_436_[+3(4.98e-07)]_\ 23 44335 1.19e-04 103_[+2(1.21e-05)]_247_\ [+3(1.50e-06)]_117 34078 1.57e-03 74_[+1(5.07e-07)]_148_\ [+1(1.45e-05)]_254 51700 1.60e-01 500 11441 1.28e-05 17_[+3(3.42e-07)]_94_[+1(5.18e-05)]_\ 213_[+2(4.31e-05)]_131 44757 4.02e-02 268_[+1(7.90e-06)]_220 45966 6.15e-07 441_[+1(8.97e-06)]_17_\ [+3(3.64e-09)]_9 45969 1.34e-03 407_[+3(7.76e-07)]_72 46005 4.73e-04 394_[+3(5.08e-06)]_17_\ [+1(4.07e-05)]_56 45124 2.85e-03 269_[+2(2.95e-07)]_219 50464 8.42e-04 51_[+2(2.35e-05)]_391_\ [+1(1.10e-05)]_34 54028 1.19e-03 204_[+3(2.94e-06)]_24_\ [+1(3.72e-05)]_239 45385 1.68e-05 130_[+2(2.35e-05)]_2_[+2(3.84e-05)]_\ 43_[+2(1.01e-07)]_123_[+1(6.73e-06)]_154 47403 1.21e-02 379_[+3(5.42e-06)]_100 48956 1.01e-02 33_[+1(1.29e-05)]_455 40441 9.10e-06 94_[+2(1.00e-06)]_319_\ [+3(3.76e-07)]_54 48823 6.58e-07 4_[+1(6.91e-05)]_30_[+2(1.84e-05)]_\ 218_[+1(9.65e-06)]_96_[+3(1.53e-07)]_95 49579 4.15e-04 238_[+2(1.01e-05)]_20_\ [+1(9.65e-06)]_218 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************