******************************************************************************** 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/146/146.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17324 1.0000 500 17414 1.0000 500 8686 1.0000 500 42774 1.0000 500 17519 1.0000 500 17545 1.0000 500 17846 1.0000 500 17954 1.0000 500 46522 1.0000 500 21073 1.0000 500 28234 1.0000 500 51018 1.0000 500 28694 1.0000 500 51066 1.0000 500 14269 1.0000 500 29177 1.0000 500 48728 1.0000 500 25375 1.0000 500 15632 1.0000 500 15619 1.0000 500 30315 1.0000 500 23324 1.0000 500 30660 1.0000 500 30670 1.0000 500 23687 1.0000 500 23748 1.0000 500 18559 1.0000 500 18585 1.0000 500 51291 1.0000 500 18859 1.0000 500 19025 1.0000 500 10769 1.0000 500 19152 1.0000 500 8185 1.0000 500 50886 1.0000 500 27118 1.0000 500 27125 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/146/146.seqs.fa -oc motifs/146 -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= 37 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= 18500 N= 37 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.247 C 0.242 G 0.230 T 0.280 Background letter frequencies (from dataset with add-one prior applied): A 0.247 C 0.242 G 0.230 T 0.280 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 30 llr = 351 E-value = 4.6e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 322:::8::::1::5215654 pos.-specific C 55151::8a:722:26312:1 probability G ::42::1::621:::::::1: matrix T 22439a12:416793163135 bits 2.1 1.9 * 1.7 * * 1.5 ** * * Relative 1.3 ** ** * Entropy 1.1 ***** * (16.9 bits) 0.8 ******* ** 0.6 ******* ** ** * * 0.4 ** ******** ********* 0.2 ********************* 0.0 --------------------- Multilevel CCGCTTACCGCTTTACTAAAT consensus AATT T CC TACTCTA sequence TA C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 19025 369 3.36e-09 GACCGAAATA CCTCTTACCGCTCTACTTCAA GTTTCTGCCC 17545 362 6.61e-09 CAGACGGGGG CCGCTTATCGCATTACTAAAA ATTGCTGGGC 30315 71 1.45e-08 CGGGTGATGT ATGGTTACCGCCTTACTACAT TTCAACCTTG 17519 314 2.25e-08 CAGTACCTAT ACCGTTACCTCTTTACTAATT TCGCGCAGCC 18585 362 2.60e-08 TTCAGTAAAA CTATTTACCGCCCTACTAAAA TTTGCAGTCG 17846 390 5.90e-08 TAGTGTTTAC CTTCTTACCTCTTTACTTCGT ACAGACCGGC 19152 366 1.60e-07 GGTATGTAGA TTTCTTACCGCCTTACTAACT TTATTTCACA 17324 338 2.02e-07 TACGGGTCAA AATCTTACCGCGTTTACTAAA ATATGGACTA 50886 327 2.27e-07 AGCGCCCTGT CCAATTACCTGTTTACTAATT TCGGGAACAG 8185 84 2.27e-07 TTAGTTTCTA CCTTCTACCGCTTTTACTAAT GTACGACAGT 51018 440 2.54e-07 TGAGGCTTTA CCTCTTACCGTTTTTTCTATT TTCTGGATTT 8686 146 3.55e-07 TAAACGAAAT CATTTTACCTCTCTTACTAAA AGACACCACC 27125 36 4.41e-07 GGATGTTTTA CCACTTTTCGCTTTACTCAAA TGAGCAGCAT 15632 349 4.41e-07 AGTGTCTTAC CTGTTTACCGTGTTACTAAAC CATGGAACAG 27118 231 7.43e-07 AAACAGCATC AATCTTACCGCGCTTACTAAA TTCCTTCCCT 51066 2 7.43e-07 C ACACTTACCTGCATACTAAAA GTCTTTGTCA 28234 330 9.08e-07 GGTGTACTCC CGGTTTACCTCCTTACTATTT TCATTCCACC 29177 104 1.22e-06 ATAATGGCGC AAGGTTACCGCTGTACTATTT TATATTGTGT 23324 463 1.47e-06 TTCCGCTACT ACTTTTATCTCATTCACAAAA CACATTCCCT 17954 80 2.13e-06 AAATTGCTTT TCGCTTGTCGCATTCCCAATT CCTTCCATCA 21073 320 2.55e-06 GCAGTAAAAC GCCTTTACCGCTTTACTAGTT ACTAAACAAA 17414 342 3.93e-06 TTGTTCGACT AATCTTACCGCTTACTAAAAT CTCGAAATCA 25375 393 5.48e-06 TCGTAAAATA CCACTTACACTTTTACTAAAA GTTTCCGTGC 51291 215 5.94e-06 TTGCAAATCT TAGTTTACCTCTTTACCGCTC TTACTTTGCA 18559 320 6.43e-06 GCTAAATTTA CCTGTTACCGCTTTCTACTTT TTTCTTGGCT 15619 13 1.02e-05 CTCTCTCGAC ACACTTGTCGGTTTTATTAGT TAGGTACGAA 23687 379 4.60e-05 TTCCGTCCCT TTGCTTACCTCTCGCAAAAAC CAACGCATGC 48728 470 4.89e-05 CGTTCATCCA TAGGTTTCCTGCTTTCCCCAA CACTATTACC 30670 429 6.98e-05 AGTCTCTGAC ACGTTGGCCGTTTTCTTTCTT TCGTTTCTTC 18859 375 1.66e-04 CCCCACGCCC CTGCCTGCCTGCCTTCCCCGT GCACCACCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19025 3.4e-09 368_[+1]_111 17545 6.6e-09 361_[+1]_118 30315 1.4e-08 70_[+1]_409 17519 2.3e-08 313_[+1]_166 18585 2.6e-08 361_[+1]_118 17846 5.9e-08 389_[+1]_90 19152 1.6e-07 365_[+1]_114 17324 2e-07 337_[+1]_142 50886 2.3e-07 326_[+1]_153 8185 2.3e-07 83_[+1]_396 51018 2.5e-07 439_[+1]_40 8686 3.6e-07 145_[+1]_334 27125 4.4e-07 35_[+1]_444 15632 4.4e-07 348_[+1]_131 27118 7.4e-07 230_[+1]_249 51066 7.4e-07 1_[+1]_478 28234 9.1e-07 329_[+1]_150 29177 1.2e-06 103_[+1]_376 23324 1.5e-06 462_[+1]_17 17954 2.1e-06 79_[+1]_400 21073 2.5e-06 319_[+1]_160 17414 3.9e-06 341_[+1]_138 25375 5.5e-06 392_[+1]_87 51291 5.9e-06 214_[+1]_265 18559 6.4e-06 319_[+1]_160 15619 1e-05 12_[+1]_467 23687 4.6e-05 378_[+1]_101 48728 4.9e-05 469_[+1]_10 30670 7e-05 428_[+1]_51 18859 0.00017 374_[+1]_105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=30 19025 ( 369) CCTCTTACCGCTCTACTTCAA 1 17545 ( 362) CCGCTTATCGCATTACTAAAA 1 30315 ( 71) ATGGTTACCGCCTTACTACAT 1 17519 ( 314) ACCGTTACCTCTTTACTAATT 1 18585 ( 362) CTATTTACCGCCCTACTAAAA 1 17846 ( 390) CTTCTTACCTCTTTACTTCGT 1 19152 ( 366) TTTCTTACCGCCTTACTAACT 1 17324 ( 338) AATCTTACCGCGTTTACTAAA 1 50886 ( 327) CCAATTACCTGTTTACTAATT 1 8185 ( 84) CCTTCTACCGCTTTTACTAAT 1 51018 ( 440) CCTCTTACCGTTTTTTCTATT 1 8686 ( 146) CATTTTACCTCTCTTACTAAA 1 27125 ( 36) CCACTTTTCGCTTTACTCAAA 1 15632 ( 349) CTGTTTACCGTGTTACTAAAC 1 27118 ( 231) AATCTTACCGCGCTTACTAAA 1 51066 ( 2) ACACTTACCTGCATACTAAAA 1 28234 ( 330) CGGTTTACCTCCTTACTATTT 1 29177 ( 104) AAGGTTACCGCTGTACTATTT 1 23324 ( 463) ACTTTTATCTCATTCACAAAA 1 17954 ( 80) TCGCTTGTCGCATTCCCAATT 1 21073 ( 320) GCCTTTACCGCTTTACTAGTT 1 17414 ( 342) AATCTTACCGCTTACTAAAAT 1 25375 ( 393) CCACTTACACTTTTACTAAAA 1 51291 ( 215) TAGTTTACCTCTTTACCGCTC 1 18559 ( 320) CCTGTTACCGCTTTCTACTTT 1 15619 ( 13) ACACTTGTCGGTTTTATTAGT 1 23687 ( 379) TTGCTTACCTCTCGCAAAAAC 1 48728 ( 470) TAGGTTTCCTGCTTTCCCCAA 1 30670 ( 429) ACGTTGGCCGTTTTCTTTCTT 1 18859 ( 375) CTGCCTGCCTGCCTTCCCCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 10.914 E= 4.6e-020 43 95 -278 -75 -8 104 -278 -26 -31 -186 67 39 -289 104 -47 10 -1155 -186 -1155 174 -1155 -1155 -278 179 169 -1155 -79 -207 -1155 178 -1155 -75 -289 200 -1155 -1155 -1155 -286 138 39 -1155 153 -47 -107 -131 -5 -120 102 -289 -28 -278 139 -289 -1155 -278 174 111 -28 -1155 -7 -8 139 -1155 -107 -131 46 -1155 102 111 -86 -278 10 136 -5 -278 -149 111 -286 -120 25 57 -128 -1155 93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 30 E= 4.6e-020 0.333333 0.466667 0.033333 0.166667 0.233333 0.500000 0.033333 0.233333 0.200000 0.066667 0.366667 0.366667 0.033333 0.500000 0.166667 0.300000 0.000000 0.066667 0.000000 0.933333 0.000000 0.000000 0.033333 0.966667 0.800000 0.000000 0.133333 0.066667 0.000000 0.833333 0.000000 0.166667 0.033333 0.966667 0.000000 0.000000 0.000000 0.033333 0.600000 0.366667 0.000000 0.700000 0.166667 0.133333 0.100000 0.233333 0.100000 0.566667 0.033333 0.200000 0.033333 0.733333 0.033333 0.000000 0.033333 0.933333 0.533333 0.200000 0.000000 0.266667 0.233333 0.633333 0.000000 0.133333 0.100000 0.333333 0.000000 0.566667 0.533333 0.133333 0.033333 0.300000 0.633333 0.233333 0.033333 0.100000 0.533333 0.033333 0.100000 0.333333 0.366667 0.100000 0.000000 0.533333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][CAT][GTA][CT]TTACC[GT]C[TC][TC]T[ATC][CA][TC][AT][AC][AT][TA] -------------------------------------------------------------------------------- Time 12.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 11 llr = 129 E-value = 7.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 5:::a:5:1:a2 pos.-specific C :71::9::1::1 probability G 13:a:::a2a:5 matrix T 4:9::15:6::2 bits 2.1 ** * ** 1.9 ** * ** 1.7 ** * ** 1.5 **** * ** Relative 1.3 ***** * ** Entropy 1.1 ***** * ** (17.0 bits) 0.8 ******* ** 0.6 ******** ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACTGACAGTGAG consensus TG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 17846 246 4.78e-08 TATCTCGATT ACTGACAGTGAG TGCCTTCGTT 23748 208 2.63e-07 ATATAGAAAA AGTGACAGTGAG TTCCTAAAAA 28694 370 4.64e-07 TTTCATTCGG AGTGACTGTGAG ACGACACGCA 27125 13 7.28e-07 AATTTTTTGC ACTGACTGTGAT AGGATGTTTT 19025 221 2.10e-06 TCTTCATTGG AGTGACTGTGAA TCCGCTCGCG 19152 211 2.86e-06 TCAAAATGCA TCTGACAGGGAA TACGCAGATT 42774 488 2.86e-06 TGTAATTAAC TCTGACTGTGAC C 15632 418 3.07e-06 GCCGCTTCAG TCTGACAGGGAT TCCTCGTCGG 17545 219 3.48e-06 TTGACTCTTT TCTGATAGTGAG GCTCCGTCGG 21073 208 6.67e-06 ATCGATTTTT GCTGACTGAGAG ACAAACGAAG 18559 443 7.81e-06 TCTCTCATCA ACCGACAGCGAG CGTGATTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17846 4.8e-08 245_[+2]_243 23748 2.6e-07 207_[+2]_281 28694 4.6e-07 369_[+2]_119 27125 7.3e-07 12_[+2]_476 19025 2.1e-06 220_[+2]_268 19152 2.9e-06 210_[+2]_278 42774 2.9e-06 487_[+2]_1 15632 3.1e-06 417_[+2]_71 17545 3.5e-06 218_[+2]_270 21073 6.7e-06 207_[+2]_281 18559 7.8e-06 442_[+2]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=11 17846 ( 246) ACTGACAGTGAG 1 23748 ( 208) AGTGACAGTGAG 1 28694 ( 370) AGTGACTGTGAG 1 27125 ( 13) ACTGACTGTGAT 1 19025 ( 221) AGTGACTGTGAA 1 19152 ( 211) TCTGACAGGGAA 1 42774 ( 488) TCTGACTGTGAC 1 15632 ( 418) TCTGACAGGGAT 1 17545 ( 219) TCTGATAGTGAG 1 21073 ( 208) GCTGACTGAGAG 1 18559 ( 443) ACCGACAGCGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18093 bayes= 11.7098 E= 7.2e+001 114 -1010 -134 38 -1010 158 24 -1010 -1010 -141 -1010 170 -1010 -1010 212 -1010 201 -1010 -1010 -1010 -1010 191 -1010 -162 114 -1010 -1010 70 -1010 -1010 212 -1010 -144 -141 -34 118 -1010 -1010 212 -1010 201 -1010 -1010 -1010 -44 -141 124 -62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 7.2e+001 0.545455 0.000000 0.090909 0.363636 0.000000 0.727273 0.272727 0.000000 0.000000 0.090909 0.000000 0.909091 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.909091 0.000000 0.090909 0.545455 0.000000 0.000000 0.454545 0.000000 0.000000 1.000000 0.000000 0.090909 0.090909 0.181818 0.636364 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.181818 0.090909 0.545455 0.181818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][CG]TGAC[AT]GTGAG -------------------------------------------------------------------------------- Time 26.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 31 llr = 262 E-value = 5.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::4388:28897 pos.-specific C 56142:a1:2:1 probability G 4443:2:72:11 matrix T 212::::::::1 bits 2.1 1.9 * 1.7 * 1.5 * * * * Relative 1.3 *** *** Entropy 1.1 ******* (12.2 bits) 0.8 * ******* 0.6 * ******** 0.4 ** ********* 0.2 ************ 0.0 ------------ Multilevel CCACAACGAAAA consensus GGGA C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 51291 193 2.48e-07 AAATAAGTAC GCGCAACGAAAA TTGCAAATCT 30660 370 5.76e-07 TTTGTTTCAT GCAAAACGAAAA ATCAAACTTT 17324 24 2.04e-06 AAACATATTT GCTGAACGAAAA GGCAAAGCGG 19025 68 3.18e-06 GGAAAAGGCT CCACCACGAAAA AGCCGAAGCG 18859 90 3.18e-06 AGAAGAACGA CGACAACGACAA ACCGAGATGG 23687 182 4.58e-06 ATGGCATCAT GCCAAACGAAAA AGCACCTGCA 51018 275 1.04e-05 TTGTTCACAT CGACAACGAAAG GCGCGATACC 15619 40 1.43e-05 TAGTTAGGTA CGAAAACGAAGA CACAAGAGGA 28694 233 1.78e-05 GTCGGAATTT TCGAAACGGAAA GGTAGTCACG 30315 151 2.00e-05 ACGACTACGA CGACAACAACAA CATCGTTCGT 8185 359 2.17e-05 TTGATTTGTT GCGAAGCGACAA ACGTAGGCTC 48728 53 2.17e-05 GCGAGAAAGG CCGGAACAGAAA GGCTGACGAA 17954 477 2.76e-05 ATCCAACTCT CCGGAACGACAC AAATAGGCCA 28234 170 3.81e-05 GGCCGGCGTT CGACAACGACAC AAATCAAAAC 17846 208 4.23e-05 TTTCCATCGT CCGCCACCAAAA TACTGGAGCG 23748 417 4.78e-05 CTTTTTCGCA GCAGAGCGAAAC TGCGCTCCCT 18585 113 5.25e-05 AAGCACGAAC TCGCAGCAAAAA TCGGAGGGCA 18559 67 6.90e-05 AATGTAGTCA TGTCAACGGAAA AGGCAAACAG 30670 348 6.90e-05 AAAGGACTGG GTAGAACAAAAA GATTCCTTTC 17545 389 6.90e-05 AAAAATTGCT GGGCAGCCAAAA ACTGGGGCCT 23324 349 7.49e-05 TAAACTTAGT GCCTAACGAAAA GCACGTTGGT 17519 202 8.20e-05 CATCGTTGTT GGAAAGCGAAGA ATCTGGAATG 8686 134 9.54e-05 TAACTCTATC TCTAAACGAAAT CATTTTACCT 10769 236 1.12e-04 TTTGTTTGAA CCTAAGCGAAAG ATTACTCGCT 21073 412 1.12e-04 CGTGCGTGCT TGTCAACGAAAT CCACCCCTCT 50886 80 1.55e-04 CGGACTACGC TCGGAACGAAGG AAACCCCTAA 29177 174 1.81e-04 GTGTGCGAGG CCGGCACGGAGA CCGTCAAGTC 25375 457 2.10e-04 GGCAACAGGA GGGGAACAACAT ACAGTATTGA 42774 438 2.10e-04 AGGATTGTTC CGACAATAAAAA TCCGATCAAA 17414 383 2.24e-04 CGCTTGACCT CTCGCACGAAAA TTTTTGCTGC 27118 356 4.44e-04 TCTGTTCGAA CCAACACCGCAA ACACTATTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 51291 2.5e-07 192_[+3]_296 30660 5.8e-07 369_[+3]_119 17324 2e-06 23_[+3]_465 19025 3.2e-06 67_[+3]_421 18859 3.2e-06 89_[+3]_399 23687 4.6e-06 181_[+3]_307 51018 1e-05 274_[+3]_214 15619 1.4e-05 39_[+3]_449 28694 1.8e-05 232_[+3]_256 30315 2e-05 150_[+3]_338 8185 2.2e-05 358_[+3]_130 48728 2.2e-05 52_[+3]_436 17954 2.8e-05 476_[+3]_12 28234 3.8e-05 169_[+3]_319 17846 4.2e-05 207_[+3]_281 23748 4.8e-05 416_[+3]_72 18585 5.2e-05 112_[+3]_376 18559 6.9e-05 66_[+3]_422 30670 6.9e-05 347_[+3]_141 17545 6.9e-05 388_[+3]_100 23324 7.5e-05 348_[+3]_140 17519 8.2e-05 201_[+3]_287 8686 9.5e-05 133_[+3]_355 10769 0.00011 235_[+3]_253 21073 0.00011 411_[+3]_77 50886 0.00016 79_[+3]_409 29177 0.00018 173_[+3]_315 25375 0.00021 456_[+3]_32 42774 0.00021 437_[+3]_51 17414 0.00022 382_[+3]_106 27118 0.00044 355_[+3]_133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=31 51291 ( 193) GCGCAACGAAAA 1 30660 ( 370) GCAAAACGAAAA 1 17324 ( 24) GCTGAACGAAAA 1 19025 ( 68) CCACCACGAAAA 1 18859 ( 90) CGACAACGACAA 1 23687 ( 182) GCCAAACGAAAA 1 51018 ( 275) CGACAACGAAAG 1 15619 ( 40) CGAAAACGAAGA 1 28694 ( 233) TCGAAACGGAAA 1 30315 ( 151) CGACAACAACAA 1 8185 ( 359) GCGAAGCGACAA 1 48728 ( 53) CCGGAACAGAAA 1 17954 ( 477) CCGGAACGACAC 1 28234 ( 170) CGACAACGACAC 1 17846 ( 208) CCGCCACCAAAA 1 23748 ( 417) GCAGAGCGAAAC 1 18585 ( 113) TCGCAGCAAAAA 1 18559 ( 67) TGTCAACGGAAA 1 30670 ( 348) GTAGAACAAAAA 1 17545 ( 389) GGGCAGCCAAAA 1 23324 ( 349) GCCTAACGAAAA 1 17519 ( 202) GGAAAGCGAAGA 1 8686 ( 134) TCTAAACGAAAT 1 10769 ( 236) CCTAAGCGAAAG 1 21073 ( 412) TGTCAACGAAAT 1 50886 ( 80) TCGGAACGAAGG 1 29177 ( 174) CCGGCACGGAGA 1 25375 ( 457) GGGGAACAACAT 1 42774 ( 438) CGACAATAAAAA 1 17414 ( 383) CTCGCACGAAAA 1 27118 ( 356) CCAACACCGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 18093 bayes= 9.14965 E= 5.2e+001 -1160 90 62 -53 -1160 126 62 -212 65 -132 62 -80 23 68 33 -311 176 -59 -1160 -1160 170 -1160 -25 -1160 -1160 200 -1160 -311 -35 -132 162 -1160 176 -1160 -51 -1160 165 -10 -1160 -1160 182 -1160 -83 -1160 152 -132 -125 -153 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 31 E= 5.2e+001 0.000000 0.451613 0.354839 0.193548 0.000000 0.580645 0.354839 0.064516 0.387097 0.096774 0.354839 0.161290 0.290323 0.387097 0.290323 0.032258 0.838710 0.161290 0.000000 0.000000 0.806452 0.000000 0.193548 0.000000 0.000000 0.967742 0.000000 0.032258 0.193548 0.096774 0.709677 0.000000 0.838710 0.000000 0.161290 0.000000 0.774194 0.225806 0.000000 0.000000 0.870968 0.000000 0.129032 0.000000 0.709677 0.096774 0.096774 0.096774 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][CG][AG][CAG]AACGA[AC]AA -------------------------------------------------------------------------------- Time 40.08 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17324 7.14e-06 23_[+3(2.04e-06)]_1_[+3(3.45e-05)]_\ 27_[+1(7.40e-05)]_241_[+1(2.02e-07)]_142 17414 5.45e-03 341_[+1(3.93e-06)]_138 8686 4.05e-04 133_[+3(9.54e-05)]_[+1(3.55e-07)]_\ 334 42774 4.25e-03 487_[+2(2.86e-06)]_1 17519 5.07e-05 201_[+3(8.20e-05)]_100_\ [+1(2.25e-08)]_166 17545 4.92e-08 218_[+2(3.48e-06)]_131_\ [+1(6.61e-09)]_6_[+3(6.90e-05)]_100 17846 4.60e-09 207_[+3(4.23e-05)]_26_\ [+2(4.78e-08)]_132_[+1(5.90e-08)]_90 17954 4.43e-04 79_[+1(2.13e-06)]_376_\ [+3(2.76e-05)]_12 46522 5.70e-01 500 21073 2.85e-05 207_[+2(6.67e-06)]_100_\ [+1(2.55e-06)]_160 28234 4.39e-04 169_[+3(3.81e-05)]_148_\ [+1(9.08e-07)]_150 51018 5.56e-05 274_[+3(1.04e-05)]_153_\ [+1(2.54e-07)]_40 28694 1.69e-04 232_[+3(1.78e-05)]_125_\ [+2(4.64e-07)]_119 51066 8.89e-03 1_[+1(7.43e-07)]_478 14269 6.61e-01 500 29177 1.84e-03 103_[+1(1.22e-06)]_376 48728 1.06e-02 52_[+3(2.17e-05)]_405_\ [+1(4.89e-05)]_10 25375 9.70e-03 392_[+1(5.48e-06)]_87 15632 3.84e-05 348_[+1(4.41e-07)]_48_\ [+2(3.07e-06)]_71 15619 4.95e-04 12_[+1(1.02e-05)]_6_[+3(1.43e-05)]_\ 449 30315 7.69e-06 70_[+1(1.45e-08)]_59_[+3(2.00e-05)]_\ 338 23324 1.12e-03 348_[+3(7.49e-05)]_102_\ [+1(1.47e-06)]_17 30660 7.18e-03 369_[+3(5.76e-07)]_119 30670 2.98e-02 347_[+3(6.90e-05)]_69_\ [+1(6.98e-05)]_51 23687 2.09e-03 181_[+3(4.58e-06)]_185_\ [+1(4.60e-05)]_101 23748 2.49e-04 207_[+2(2.63e-07)]_197_\ [+3(4.78e-05)]_72 18559 4.86e-05 66_[+3(6.90e-05)]_241_\ [+1(6.43e-06)]_102_[+2(7.81e-06)]_46 18585 5.76e-06 112_[+3(5.25e-05)]_237_\ [+1(2.60e-08)]_118 51291 2.73e-05 192_[+3(2.48e-07)]_10_\ [+1(5.94e-06)]_265 18859 5.52e-03 89_[+3(3.18e-06)]_399 19025 9.89e-10 67_[+3(3.18e-06)]_141_\ [+2(2.10e-06)]_136_[+1(3.36e-09)]_111 10769 3.47e-01 500 19152 8.59e-06 210_[+2(2.86e-06)]_143_\ [+1(1.60e-07)]_114 8185 1.88e-05 83_[+1(2.27e-07)]_254_\ [+3(2.17e-05)]_130 50886 1.90e-04 326_[+1(2.27e-07)]_153 27118 3.60e-03 230_[+1(7.43e-07)]_249 27125 5.30e-06 12_[+2(7.28e-07)]_11_[+1(4.41e-07)]_\ 100_[+2(6.67e-06)]_332 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************