******************************************************************************** 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/151/151.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9199 1.0000 500 31919 1.0000 500 43162 1.0000 500 28147 1.0000 500 46735 1.0000 500 13361 1.0000 500 28359 1.0000 500 21323 1.0000 500 13682 1.0000 500 28562 1.0000 500 21659 1.0000 500 28979 1.0000 500 47804 1.0000 500 29097 1.0000 500 48411 1.0000 500 48699 1.0000 500 22774 1.0000 500 50701 1.0000 500 39687 1.0000 500 30160 1.0000 500 23079 1.0000 500 15740 1.0000 500 30262 1.0000 500 16125 1.0000 500 30486 1.0000 500 23691 1.0000 500 50259 1.0000 500 31073 1.0000 500 25577 1.0000 500 43840 1.0000 500 25714 1.0000 500 10196 1.0000 500 11032 1.0000 500 44291 1.0000 500 34146 1.0000 500 19314 1.0000 500 19413 1.0000 500 11126 1.0000 500 19615 1.0000 500 26849 1.0000 500 26975 1.0000 500 6847 1.0000 500 36226 1.0000 500 27851 1.0000 500 44971 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/151/151.seqs.fa -oc motifs/151 -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= 45 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= 22500 N= 45 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.249 C 0.252 G 0.220 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.249 C 0.252 G 0.220 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 34 llr = 414 E-value = 1.0e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 116214:::6:::::::81: pos.-specific C 31168:6111891652::83 probability G :211:42::::162:2:::: matrix T 55311329922:2256a2:7 bits 2.2 2.0 1.7 * 1.5 * * Relative 1.3 ** ** *** Entropy 1.1 * ** ** *** (17.6 bits) 0.9 * ** ** * **** 0.7 ** ******* ****** 0.4 * ****************** 0.2 ******************** 0.0 -------------------- Multilevel TTACCGCTTACCGCCTTACT consensus CGTA AG TT TGTC T C sequence TT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 43162 46 4.14e-10 AACTTTACAG TTACCACTTACCGCTTTTCT GAAACTCGAA 43840 324 2.21e-09 CTCGTAGTGT TTACCTCTTACCTCCGTACT TCGTAGAGGC 21323 345 4.30e-09 ATTTCCAAGT TTACCACTCACCGCTTTACT ATCGCCAATC 31919 406 8.01e-09 TACATCCGAT GTACCGCTTACCGCCGTACT CAGGAAGGAG 22774 330 1.44e-08 TGGTTTGGAG TTACCGCTTTTCGTCTTACT AACAACACCA 30262 327 1.66e-08 GCTGTGACTA TGAACTGTTACCGGCTTACT ATTTTTTGAA 36226 36 2.51e-08 GGCCATCGCA CGTACAGTTACCGCCTTACT TGGAACTCCC 19413 77 3.71e-08 GTTTTCATGT TTACCTCTTTTCTCCTTACT GATTTTCGCT 11032 213 5.45e-08 GCATTAGCGT TTACCACTTTTCGGTCTACT CGAAACTACG 10196 137 8.86e-08 CCCTAAAGGG CTATCTTTTACCGGCTTACT AAACCTGCGC 30160 105 1.76e-07 ATGGAAAGTT CCTCAACTTACCGCCCTACT AGAACATGAA 47804 97 1.76e-07 GCCATCACCG TTACCGCTTTTCCCTGTACT AAAACCCCAC 31073 330 2.19e-07 CTAGTTGCTT TTACCGCCTCTCGCTTTACT AACTTTTTGT 34146 206 2.44e-07 CGGAGCACAT TTTACAGTTACCGACTTACT AAATTCAATA 48411 376 2.44e-07 GGTTGTCTTG CTACCGGTTACCGCTGTTAC TGTTTCCCCG 23079 321 2.71e-07 TCCGGGTGAG AACACTCTTACCGCTTTACT CAAATCATTC 19615 61 5.54e-07 TGCATTCCCG AATAATCTTACCGCTTTACT TGATTTGGAA 29097 319 1.29e-06 CCGTTAGCTT TTACCACTTACACGCCTACT TGGTTTTTTC 19314 367 1.41e-06 TTCGACCAAG TTACCTTGTTTCGCTTTACT AAACTTGGAG 16125 24 2.00e-06 AATACTATAC AGACAGGTTTCCTGTTTACC GTTTACCGTC 50259 45 2.17e-06 GGCTTTGCTA CCACCGTTTACCGTCTCACC ACACTTACTA 50701 163 3.85e-06 GAGACCATCT TTTCCAGTTACCCCCGTTAC TAAAAGCCGT 28979 341 3.85e-06 AAGATTCAGT TTACCGCTTACCAGCCTTAC TTATTCAGGT 46735 216 3.85e-06 CTAACATCGT TTACCGTTCACCGCTCTTAC TAGTGCACTT 30486 351 4.51e-06 TGAACTCATA ACCGCACTTACCTGTTTACT ACAAACAAAC 39687 326 4.51e-06 GTGGGACTGG CAGTAATTTACCGCCTTACT AAAATTGCAT 21659 206 4.87e-06 AATACGCTCA CACAATGTTACCTCTTTACT ATTTTTCGAG 9199 227 8.20e-06 ACCGTCAACT CGACTGCTTCCCGTCGTTCC CTCCAGTTGT 6847 151 9.45e-06 AAGGACCCCG TATCCGCTTTCCTTTCTAGT AGTTTCTGTA 25577 176 1.09e-05 GGTAGGTTGG TGGTCTTTTCCCGCCCTACC CTATTCAACC 13361 436 1.09e-05 ACACCTTTCT CCTCCACTTTTGGTTTTACC CCATTACCGC 27851 320 1.53e-05 AAGAGTGACA TTACCGCTTACTTTCGTTAC TTGCCATACT 26849 134 1.86e-05 TATACTCAAT CGTGTGTCTACCGCTTTACT AAAAAGTGCT 15740 472 3.45e-05 GTTTTGTGCA AGTACAGTTCCGTGTTTACC GCCAGTATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43162 4.1e-10 45_[+1]_435 43840 2.2e-09 323_[+1]_157 21323 4.3e-09 344_[+1]_136 31919 8e-09 405_[+1]_75 22774 1.4e-08 329_[+1]_151 30262 1.7e-08 326_[+1]_154 36226 2.5e-08 35_[+1]_445 19413 3.7e-08 76_[+1]_404 11032 5.5e-08 212_[+1]_268 10196 8.9e-08 136_[+1]_344 30160 1.8e-07 104_[+1]_376 47804 1.8e-07 96_[+1]_384 31073 2.2e-07 329_[+1]_151 34146 2.4e-07 205_[+1]_275 48411 2.4e-07 375_[+1]_105 23079 2.7e-07 320_[+1]_160 19615 5.5e-07 60_[+1]_420 29097 1.3e-06 318_[+1]_162 19314 1.4e-06 366_[+1]_114 16125 2e-06 23_[+1]_457 50259 2.2e-06 44_[+1]_436 50701 3.9e-06 162_[+1]_318 28979 3.9e-06 340_[+1]_140 46735 3.9e-06 215_[+1]_265 30486 4.5e-06 350_[+1]_130 39687 4.5e-06 325_[+1]_155 21659 4.9e-06 205_[+1]_275 9199 8.2e-06 226_[+1]_254 6847 9.5e-06 150_[+1]_330 25577 1.1e-05 175_[+1]_305 13361 1.1e-05 435_[+1]_45 27851 1.5e-05 319_[+1]_161 26849 1.9e-05 133_[+1]_347 15740 3.4e-05 471_[+1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=34 43162 ( 46) TTACCACTTACCGCTTTTCT 1 43840 ( 324) TTACCTCTTACCTCCGTACT 1 21323 ( 345) TTACCACTCACCGCTTTACT 1 31919 ( 406) GTACCGCTTACCGCCGTACT 1 22774 ( 330) TTACCGCTTTTCGTCTTACT 1 30262 ( 327) TGAACTGTTACCGGCTTACT 1 36226 ( 36) CGTACAGTTACCGCCTTACT 1 19413 ( 77) TTACCTCTTTTCTCCTTACT 1 11032 ( 213) TTACCACTTTTCGGTCTACT 1 10196 ( 137) CTATCTTTTACCGGCTTACT 1 30160 ( 105) CCTCAACTTACCGCCCTACT 1 47804 ( 97) TTACCGCTTTTCCCTGTACT 1 31073 ( 330) TTACCGCCTCTCGCTTTACT 1 34146 ( 206) TTTACAGTTACCGACTTACT 1 48411 ( 376) CTACCGGTTACCGCTGTTAC 1 23079 ( 321) AACACTCTTACCGCTTTACT 1 19615 ( 61) AATAATCTTACCGCTTTACT 1 29097 ( 319) TTACCACTTACACGCCTACT 1 19314 ( 367) TTACCTTGTTTCGCTTTACT 1 16125 ( 24) AGACAGGTTTCCTGTTTACC 1 50259 ( 45) CCACCGTTTACCGTCTCACC 1 50701 ( 163) TTTCCAGTTACCCCCGTTAC 1 28979 ( 341) TTACCGCTTACCAGCCTTAC 1 46735 ( 216) TTACCGTTCACCGCTCTTAC 1 30486 ( 351) ACCGCACTTACCTGTTTACT 1 39687 ( 326) CAGTAATTTACCGCCTTACT 1 21659 ( 206) CACAATGTTACCTCTTTACT 1 9199 ( 227) CGACTGCTTCCCGTCGTTCC 1 6847 ( 151) TATCCGCTTTCCTTTCTAGT 1 25577 ( 176) TGGTCTTTTCCCGCCCTACC 1 13361 ( 436) CCTCCACTTTTGGTTTTACC 1 27851 ( 320) TTACCGCTTACTTTCGTTAC 1 26849 ( 134) CGTGTGTCTACCGCTTTACT 1 15740 ( 472) AGTACAGTTCCGTGTTTACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 21645 bayes= 10.6784 E= 1.0e-032 -76 22 -290 92 -76 -110 -10 92 124 -151 -190 -8 -27 136 -190 -166 -76 165 -1173 -224 50 -1173 80 -8 -1173 115 10 -44 -1173 -210 -290 171 -1173 -210 -1173 175 138 -110 -1173 -24 -1173 165 -1173 -44 -308 181 -190 -324 -308 -151 155 -24 -308 115 10 -66 -1173 99 -1173 84 -1173 -29 -10 108 -1173 -310 -1173 180 167 -1173 -1173 -44 -76 171 -290 -1173 -1173 36 -1173 128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 34 E= 1.0e-032 0.147059 0.294118 0.029412 0.529412 0.147059 0.117647 0.205882 0.529412 0.588235 0.088235 0.058824 0.264706 0.205882 0.647059 0.058824 0.088235 0.147059 0.794118 0.000000 0.058824 0.352941 0.000000 0.382353 0.264706 0.000000 0.558824 0.235294 0.205882 0.000000 0.058824 0.029412 0.911765 0.000000 0.058824 0.000000 0.941176 0.647059 0.117647 0.000000 0.235294 0.000000 0.794118 0.000000 0.205882 0.029412 0.882353 0.058824 0.029412 0.029412 0.088235 0.647059 0.235294 0.029412 0.558824 0.235294 0.176471 0.000000 0.500000 0.000000 0.500000 0.000000 0.205882 0.205882 0.588235 0.000000 0.029412 0.000000 0.970588 0.794118 0.000000 0.000000 0.205882 0.147059 0.823529 0.029412 0.000000 0.000000 0.323529 0.000000 0.676471 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC][TG][AT][CA]C[GAT][CGT]TT[AT][CT]C[GT][CG][CT][TCG]T[AT]C[TC] -------------------------------------------------------------------------------- Time 19.33 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 28 llr = 262 E-value = 6.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 31::9:7:::73 pos.-specific C :4:41a1::9:3 probability G 31:::::9::35 matrix T 4496::21a1:: bits 2.2 2.0 1.7 * ** 1.5 * *** Relative 1.3 * ** *** Entropy 1.1 * ** **** (13.5 bits) 0.9 ********* 0.7 ********** 0.4 ********** 0.2 ************ 0.0 ------------ Multilevel TTTTACAGTCAG consensus GC C T GA sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 27851 226 4.03e-07 CCTAACCTAT TTTCACAGTCAG TCAGTCCCGT 26849 366 7.21e-07 AAAAAGTTAC ATTCACAGTCAG ATCGATCAAC 26975 422 2.48e-06 TGGACCTGTA GCTCACAGTCAA GGATCGACAC 28562 36 3.31e-06 TCTCGCGTAC ACTTACAGTCAC TTAGCTAGTT 10196 37 4.63e-06 CAGTCTTGTC GCTCACTGTCAG TCAGACGGAA 31919 451 4.63e-06 TCTATCCGCC GTTTACAGTCGA AGCGCCATCT 11032 260 5.42e-06 ACCCTTGCGG TTTCACAGTCGA CGCTGCGGCA 34146 143 8.02e-06 TTCTTCCGAA TGTCACAGTCGG TCCATCGACC 22774 19 8.02e-06 GTTATTGTCA TTTTACTGTCAC AGTACCATAC 48699 474 8.02e-06 TTTTTCGTAC TTTTACTGTCAA GTCTCTTTTT 30486 296 9.22e-06 GTACTTGTCT GTTTACAGTTAG CTAACTGTGA 28359 364 9.22e-06 GACAGCGTTG GTTTACAGTTAG TAACAGCGGT 25714 354 1.06e-05 AAATCTACAC GTTTACATTCAG CACTGGAAAA 31073 184 1.06e-05 GGTGTAGAAG GATCACAGTCAA ATCAAAGAGG 16125 44 1.06e-05 CCTGTTTACC GTTTACCGTCAG TACTAACTTT 29097 148 2.04e-05 CTGGCTATCG TTTTACATTCGG TCTGACTGAA 30262 232 2.89e-05 AACGACAGCG AGTCACAGTCGC ATGACAAGTG 36226 62 3.17e-05 TACTTGGAAC TCCCACAGTCAG TCACTCACTC 11126 50 3.69e-05 AGCTACTAGC ACTCACAGTTGG TACGATTTTA 43840 100 3.69e-05 TGGTCGACAC GTTTCCAGTCGC TCTATTCCGT 44971 107 3.93e-05 AGAGGGTTTC CCTTACTGTCAG TAGATGCTAG 13682 338 4.52e-05 TGTCATAAGG TCTTGCAGTCAC ACGAGGAATT 46735 6 4.52e-05 GAGGG ACTCAAAGTCAG CAAGAAGTCC 50701 214 5.18e-05 TGCGTACCCT TGTTCCAGTCAA GGCGCCGAAC 47804 54 8.32e-05 TCTTATTTTG TATCACATTCAC ATTACAGTTA 28979 160 8.79e-05 ACACACAGCC ACGTACTGTCAG GCATGGGAAA 9199 197 9.23e-05 TATCCGGTCC AATTACCGTCAC AGCACCACAC 19413 382 1.01e-04 TGTTTTACGA TCTTCCTGTCGA GTTTCTGCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27851 4e-07 225_[+2]_263 26849 7.2e-07 365_[+2]_123 26975 2.5e-06 421_[+2]_67 28562 3.3e-06 35_[+2]_453 10196 4.6e-06 36_[+2]_452 31919 4.6e-06 450_[+2]_38 11032 5.4e-06 259_[+2]_229 34146 8e-06 142_[+2]_346 22774 8e-06 18_[+2]_470 48699 8e-06 473_[+2]_15 30486 9.2e-06 295_[+2]_193 28359 9.2e-06 363_[+2]_125 25714 1.1e-05 353_[+2]_135 31073 1.1e-05 183_[+2]_305 16125 1.1e-05 43_[+2]_445 29097 2e-05 147_[+2]_341 30262 2.9e-05 231_[+2]_257 36226 3.2e-05 61_[+2]_427 11126 3.7e-05 49_[+2]_439 43840 3.7e-05 99_[+2]_389 44971 3.9e-05 106_[+2]_382 13682 4.5e-05 337_[+2]_151 46735 4.5e-05 5_[+2]_483 50701 5.2e-05 213_[+2]_275 47804 8.3e-05 53_[+2]_435 28979 8.8e-05 159_[+2]_329 9199 9.2e-05 196_[+2]_292 19413 0.0001 381_[+2]_107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=28 27851 ( 226) TTTCACAGTCAG 1 26849 ( 366) ATTCACAGTCAG 1 26975 ( 422) GCTCACAGTCAA 1 28562 ( 36) ACTTACAGTCAC 1 10196 ( 37) GCTCACTGTCAG 1 31919 ( 451) GTTTACAGTCGA 1 11032 ( 260) TTTCACAGTCGA 1 34146 ( 143) TGTCACAGTCGG 1 22774 ( 19) TTTTACTGTCAC 1 48699 ( 474) TTTTACTGTCAA 1 30486 ( 296) GTTTACAGTTAG 1 28359 ( 364) GTTTACAGTTAG 1 25714 ( 354) GTTTACATTCAG 1 31073 ( 184) GATCACAGTCAA 1 16125 ( 44) GTTTACCGTCAG 1 29097 ( 148) TTTTACATTCGG 1 30262 ( 232) AGTCACAGTCGC 1 36226 ( 62) TCCCACAGTCAG 1 11126 ( 50) ACTCACAGTTGG 1 43840 ( 100) GTTTCCAGTCGC 1 44971 ( 107) CCTTACTGTCAG 1 13682 ( 338) TCTTGCAGTCAC 1 46735 ( 6) ACTCAAAGTCAG 1 50701 ( 214) TGTTCCAGTCAA 1 47804 ( 54) TATCACATTCAC 1 28979 ( 160) ACGTACTGTCAG 1 9199 ( 197) AATTACCGTCAC 1 19413 ( 382) TCTTCCTGTCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 22005 bayes= 10.2227 E= 6.1e-003 1 -282 55 49 -121 50 -104 62 -1145 -282 -262 174 -1145 76 -1145 103 178 -123 -262 -1145 -280 193 -1145 -1145 152 -182 -1145 -38 -1145 -1145 202 -138 -1145 -1145 -1145 184 -1145 182 -1145 -138 152 -1145 38 -1145 1 -1 118 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 28 E= 6.1e-003 0.250000 0.035714 0.321429 0.392857 0.107143 0.357143 0.107143 0.428571 0.000000 0.035714 0.035714 0.928571 0.000000 0.428571 0.000000 0.571429 0.857143 0.107143 0.035714 0.000000 0.035714 0.964286 0.000000 0.000000 0.714286 0.071429 0.000000 0.214286 0.000000 0.000000 0.892857 0.107143 0.000000 0.000000 0.000000 1.000000 0.000000 0.892857 0.000000 0.107143 0.714286 0.000000 0.285714 0.000000 0.250000 0.250000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TGA][TC]T[TC]AC[AT]GTC[AG][GAC] -------------------------------------------------------------------------------- Time 38.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 29 llr = 263 E-value = 5.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 666585a:397: pos.-specific C :1:12::2::2: probability G 4243:5:86::4 matrix T :11::::::1:6 bits 2.2 2.0 * 1.7 * 1.5 * * Relative 1.3 * ** * Entropy 1.1 * **** * * (13.1 bits) 0.9 * * ******** 0.7 * ********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel AAAAAGAGGAAT consensus G GGCA CA CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46735 186 2.98e-07 CCTCGAAACC AAAAAAAGGAAT CGGACAAGCT 19413 268 1.49e-06 TGAAATGCTA AAGAAGAGAAAG GACGATACTT 27851 301 4.97e-06 TCCCTGTGAC ACAAAAAGGAAG AGTGACATTA 43840 27 5.90e-06 TACCCTCTAG ACGAAGAGGAAG ACAACTTTTG 50701 69 6.72e-06 CGACTCTAGG AAGACAAGGAAT TTTTTATCTC 44291 234 8.05e-06 CGACACGCGA GGGGAAAGGAAG GTAAAAAGTC 28979 202 8.05e-06 AGTGAATCCA GAAGAAAGGACT TTCAATATGA 47804 282 9.25e-06 GGAGAGAGAG AGAGAGAGAAAG TTGGTTGTAG 25714 485 1.12e-05 GGTTGAGGTA AAGAAGACAAAT CACC 11126 380 1.45e-05 GTTTCGTTCG GAAGAGACAAAT TGTCGCCGCT 11032 474 1.45e-05 TATCTTTTCC AAAGAAAGAACG TTCGCATATA 21659 76 1.65e-05 TGAAAGTCAT GTAAAAAGGAAG TTTGCATTGG 21323 267 1.65e-05 ACCTTATGAC AAACAGAGGACT TTCATTTATA 26975 64 2.14e-05 GACAGTGACC AAACCAAGGAAT ATCTTTTTCC 30160 186 2.63e-05 TATTGCGATC AAGAAGAGGTAT GTGTGTCAGG 31073 19 3.08e-05 CGCAACGGGT GCAACAAGGAAT GAAAATTTAG 13361 229 3.32e-05 CATCGCCGCA GGGGAAAGGACG AAGTGAGGGA 44971 25 3.56e-05 GATGCACCAG AAGAAGAGTAAT GGTGACCTAT 13682 38 3.85e-05 GCTTTCGTGC AAGAAGAGGATT CTTCTTGAAT 43162 248 4.18e-05 TGTTGTTCGA GAAACGAGAACG ATTGATCGAT 16125 365 4.99e-05 GTTGTCGCGG GGAAAGACGACG ATGCGCTCTA 23079 472 4.99e-05 ATCAACAAAA AAGCAAACAAAG TTATTCCAGC 28359 424 5.46e-05 TCGTTTCGTT ACGCAGAGAAAG TTGAACACAC 36226 313 6.43e-05 GTCAGCTCTT GTAGAGACGAAT GCCCACCGCA 50259 296 6.43e-05 GCATTGAATC AATGCAAGGAAT GTGAAACAGC 48411 322 6.91e-05 ATGCGTTTCG GAAAAGACGTAT AGACGGACGT 9199 15 9.14e-05 CAACAGCAAC GAAACGAGCAAT ATCGTGTGTA 10196 337 9.80e-05 AGAGTAGTCA AAAGAAACGAGG CGATTTACCC 28147 172 1.21e-04 ACAACATTGG GGTGAAAGAAAT GGGGGCTCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46735 3e-07 185_[+3]_303 19413 1.5e-06 267_[+3]_221 27851 5e-06 300_[+3]_188 43840 5.9e-06 26_[+3]_462 50701 6.7e-06 68_[+3]_420 44291 8e-06 233_[+3]_255 28979 8e-06 201_[+3]_287 47804 9.2e-06 281_[+3]_207 25714 1.1e-05 484_[+3]_4 11126 1.4e-05 379_[+3]_109 11032 1.4e-05 473_[+3]_15 21659 1.7e-05 75_[+3]_413 21323 1.7e-05 266_[+3]_222 26975 2.1e-05 63_[+3]_425 30160 2.6e-05 185_[+3]_303 31073 3.1e-05 18_[+3]_470 13361 3.3e-05 228_[+3]_260 44971 3.6e-05 24_[+3]_464 13682 3.8e-05 37_[+3]_451 43162 4.2e-05 247_[+3]_241 16125 5e-05 364_[+3]_124 23079 5e-05 471_[+3]_17 28359 5.5e-05 423_[+3]_65 36226 6.4e-05 312_[+3]_176 50259 6.4e-05 295_[+3]_193 48411 6.9e-05 321_[+3]_167 9199 9.1e-05 14_[+3]_474 10196 9.8e-05 336_[+3]_152 28147 0.00012 171_[+3]_317 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=29 46735 ( 186) AAAAAAAGGAAT 1 19413 ( 268) AAGAAGAGAAAG 1 27851 ( 301) ACAAAAAGGAAG 1 43840 ( 27) ACGAAGAGGAAG 1 50701 ( 69) AAGACAAGGAAT 1 44291 ( 234) GGGGAAAGGAAG 1 28979 ( 202) GAAGAAAGGACT 1 47804 ( 282) AGAGAGAGAAAG 1 25714 ( 485) AAGAAGACAAAT 1 11126 ( 380) GAAGAGACAAAT 1 11032 ( 474) AAAGAAAGAACG 1 21659 ( 76) GTAAAAAGGAAG 1 21323 ( 267) AAACAGAGGACT 1 26975 ( 64) AAACCAAGGAAT 1 30160 ( 186) AAGAAGAGGTAT 1 31073 ( 19) GCAACAAGGAAT 1 13361 ( 229) GGGGAAAGGACG 1 44971 ( 25) AAGAAGAGTAAT 1 13682 ( 38) AAGAAGAGGATT 1 43162 ( 248) GAAACGAGAACG 1 16125 ( 365) GGAAAGACGACG 1 23079 ( 472) AAGCAAACAAAG 1 28359 ( 424) ACGCAGAGAAAG 1 36226 ( 313) GTAGAGACGAAT 1 50259 ( 296) AATGCAAGGAAT 1 48411 ( 322) GAAAAGACGTAT 1 9199 ( 15) GAAACGAGCAAT 1 10196 ( 337) AAAGAAACGAGG 1 28147 ( 172) GGTGAAAGAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 22005 bayes= 10.2071 E= 5.8e+001 124 -1150 91 -1150 132 -87 -35 -201 115 -1150 78 -201 106 -87 65 -1150 167 -29 -1150 -1150 96 -1150 123 -1150 201 -1150 -1150 -1150 -1150 -6 178 -1150 32 -287 149 -301 190 -1150 -1150 -201 154 -29 -267 -301 -1150 -1150 103 98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 29 E= 5.8e+001 0.586207 0.000000 0.413793 0.000000 0.620690 0.137931 0.172414 0.068966 0.551724 0.000000 0.379310 0.068966 0.517241 0.137931 0.344828 0.000000 0.793103 0.206897 0.000000 0.000000 0.482759 0.000000 0.517241 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.241379 0.758621 0.000000 0.310345 0.034483 0.620690 0.034483 0.931034 0.000000 0.000000 0.068966 0.724138 0.206897 0.034483 0.034483 0.000000 0.000000 0.448276 0.551724 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG]A[AG][AG][AC][GA]A[GC][GA]A[AC][TG] -------------------------------------------------------------------------------- Time 57.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9199 6.24e-04 14_[+3(9.14e-05)]_170_\ [+2(9.23e-05)]_18_[+1(8.20e-06)]_254 31919 9.41e-07 405_[+1(8.01e-09)]_25_\ [+2(4.63e-06)]_38 43162 6.73e-08 45_[+1(4.14e-10)]_182_\ [+3(4.18e-05)]_241 28147 3.55e-01 500 46735 1.18e-06 5_[+2(4.52e-05)]_168_[+3(2.98e-07)]_\ 18_[+1(3.85e-06)]_265 13361 2.33e-03 228_[+3(3.32e-05)]_195_\ [+1(1.09e-05)]_45 28359 3.68e-03 363_[+2(9.22e-06)]_48_\ [+3(5.46e-05)]_65 21323 6.06e-07 266_[+3(1.65e-05)]_66_\ [+1(4.30e-09)]_136 13682 1.06e-02 37_[+3(3.85e-05)]_288_\ [+2(4.52e-05)]_151 28562 7.76e-03 35_[+2(3.31e-06)]_453 21659 4.30e-04 75_[+3(1.65e-05)]_118_\ [+1(4.87e-06)]_275 28979 3.93e-05 159_[+2(8.79e-05)]_30_\ [+3(8.05e-06)]_127_[+1(3.85e-06)]_140 47804 2.76e-06 53_[+2(8.32e-05)]_31_[+1(1.76e-07)]_\ 165_[+3(9.25e-06)]_207 29097 2.15e-04 147_[+2(2.04e-05)]_159_\ [+1(1.29e-06)]_162 48411 1.15e-04 321_[+3(6.91e-05)]_42_\ [+1(2.44e-07)]_105 48699 6.77e-02 445_[+2(4.52e-05)]_16_\ [+2(8.02e-06)]_15 22774 1.78e-06 18_[+2(8.02e-06)]_299_\ [+1(1.44e-08)]_151 50701 2.13e-05 68_[+3(6.72e-06)]_82_[+1(3.85e-06)]_\ 31_[+2(5.18e-05)]_275 39687 1.06e-02 325_[+1(4.51e-06)]_155 30160 4.21e-05 104_[+1(1.76e-07)]_61_\ [+3(2.63e-05)]_303 23079 2.43e-04 320_[+1(2.71e-07)]_131_\ [+3(4.99e-05)]_17 15740 1.25e-01 471_[+1(3.45e-05)]_9 30262 7.41e-06 231_[+2(2.89e-05)]_83_\ [+1(1.66e-08)]_154 16125 1.73e-05 23_[+1(2.00e-06)]_[+2(1.06e-05)]_\ 309_[+3(4.99e-05)]_124 30486 2.95e-04 295_[+2(9.22e-06)]_43_\ [+1(4.51e-06)]_130 23691 6.74e-01 500 50259 9.65e-04 44_[+1(2.17e-06)]_231_\ [+3(6.43e-05)]_193 31073 1.58e-06 18_[+3(3.08e-05)]_153_\ [+2(1.06e-05)]_134_[+1(2.19e-07)]_151 25577 3.62e-02 175_[+1(1.09e-05)]_305 43840 1.66e-08 26_[+3(5.90e-06)]_61_[+2(3.69e-05)]_\ 212_[+1(2.21e-09)]_157 25714 1.42e-03 353_[+2(1.06e-05)]_119_\ [+3(1.12e-05)]_4 10196 9.24e-07 36_[+2(4.63e-06)]_88_[+1(8.86e-08)]_\ 180_[+3(9.80e-05)]_152 11032 1.23e-07 212_[+1(5.45e-08)]_27_\ [+2(5.42e-06)]_202_[+3(1.45e-05)]_15 44291 5.40e-02 233_[+3(8.05e-06)]_255 34146 5.52e-05 142_[+2(8.02e-06)]_51_\ [+1(2.44e-07)]_275 19314 6.34e-03 366_[+1(1.41e-06)]_114 19413 1.54e-07 76_[+1(3.71e-08)]_171_\ [+3(1.49e-06)]_221 11126 4.10e-03 49_[+2(3.69e-05)]_318_\ [+3(1.45e-05)]_109 19615 2.69e-03 60_[+1(5.54e-07)]_420 26849 5.63e-05 133_[+1(1.86e-05)]_212_\ [+2(7.21e-07)]_123 26975 8.41e-04 63_[+3(2.14e-05)]_346_\ [+2(2.48e-06)]_67 6847 1.57e-02 150_[+1(9.45e-06)]_330 36226 1.15e-06 35_[+1(2.51e-08)]_6_[+2(3.17e-05)]_\ 175_[+1(6.73e-05)]_44_[+3(6.43e-05)]_176 27851 7.35e-07 225_[+2(4.03e-07)]_63_\ [+3(4.97e-06)]_7_[+1(1.53e-05)]_161 44971 1.03e-02 24_[+3(3.56e-05)]_70_[+2(3.93e-05)]_\ 382 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************