******************************************************************************** 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/175/175.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10068 1.0000 500 10567 1.0000 500 10802 1.0000 500 1247 1.0000 500 13996 1.0000 500 17966 1.0000 500 1921 1.0000 500 1962 1.0000 500 1981 1.0000 500 24736 1.0000 500 24816 1.0000 500 25025 1.0000 500 25677 1.0000 500 260835 1.0000 500 263515 1.0000 500 264746 1.0000 500 268243 1.0000 500 31014 1.0000 500 31598 1.0000 500 31912 1.0000 500 36592 1.0000 500 36837 1.0000 500 37097 1.0000 500 3797 1.0000 500 3926 1.0000 500 39696 1.0000 500 43150 1.0000 500 4568 1.0000 500 4767 1.0000 500 5824 1.0000 500 6597 1.0000 500 6963 1.0000 500 7012 1.0000 500 7406 1.0000 500 8686 1.0000 500 bd790 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/175/175.seqs.fa -oc motifs/175 -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 0.253 C 0.239 G 0.243 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.253 C 0.239 G 0.243 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 31 llr = 335 E-value = 2.7e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 17234:325:23:4:42413 pos.-specific C 728618744771a1942666 probability G 2:::2::3::1::1::::21 matrix T 11:142:212:5:4126:1: bits 2.1 1.9 * 1.7 * 1.4 * * Relative 1.2 * * * * Entropy 1.0 * ** * * * * (15.6 bits) 0.8 * ** * * * * * 0.6 **** ** **** * ** * 0.4 **** ** ***** ****** 0.2 ******************** 0.0 -------------------- Multilevel CACCACCCACCTCACATCCC consensus AT AGCT A T CAA A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25025 297 1.04e-09 AGAAACATTG CACCTCCGCCCTCTCCTCGC GAAGCCTCAC 7012 60 3.86e-08 CTGTACAACA GACCACACACATCACATACC TCAGTCAATC 31014 456 6.83e-08 CTCGTCGGTA CACCACCGCCCTCTCACCTA CCATCCCAAC 1247 467 7.86e-08 CTCACCGTTC CCCTTCCTACCTCACATCCC AAAGATCACC 24736 479 9.01e-08 ACAGCAGCAA CAACACCTCTCTCTCTTCCC GT 8686 30 1.98e-07 TCACAGACTG CTCATCAGACCTCACATCGC GTACGTTCAT 1921 375 1.98e-07 CCGATCCGGA CACAAGCCACCCCACATCCC AACCTCACTG 13996 446 2.88e-07 TCGGCCGTCT CACATCACCTCTCCCATCCA ATCAACCACC 3926 454 3.25e-07 TCTCTCGATG CACAGCCCCTCTCTTTTCCC ATCGTTTCTA 37097 462 5.86e-07 TCCGTCGGCT CTCCGCAAACCTCCCCTCCC TCTACACACC 36837 94 6.56e-07 TCCGCCGGCC CTCCTCCCTCCTCACAAAGC GAGAGGACTG 1981 476 1.02e-06 CCGCTCACAT CACAGTACACCACACAACCA ACACA 43150 475 1.27e-06 GCCGTCAACT GACCTCCGCCGACTCCCCCA TCACCG 263515 481 1.56e-06 TTTCCTCATC AACAACCCACCACACTCACA 7406 309 2.12e-06 TCCTCCTCTC CAACATACACCACTCATAAC CACAAAGAAG 264746 440 4.60e-06 AACATCTTGC CCCCCCCCATCACCCATACA CATCCATCAC 10802 296 5.53e-06 GATGTTAGGA CATCACCTCCCTCGCTCCGC TCATTCACAC 6963 35 6.62e-06 GAAGATGATT CACCACCGCCACCGCCACGG CCTGCGCCAC 31912 210 6.62e-06 CAGTACCACC GCCCACCGCTGACACAAACC GAAAGATACC 36592 456 7.23e-06 CTCTTTTCCC CACCTCCTCCCCCTTCCATC ACACTCTTCC 6597 380 8.61e-06 AATCTACCAA CACGTCACACAACACAAAGC TACAATGAAG 3797 449 1.21e-05 AGAGTGATAT CCACATCAACATCACCTCTC CTCTTCCTCA 10567 199 1.21e-05 AGGCAACGGC AGCAACCCTCCTCTCTTACC AGTGGAGGAT 1962 165 1.67e-05 GCAGCAGTTA GACCACCGATGCCTCCACCG ACGACTGCGA 25677 417 2.29e-05 GTGTCCCGCC GTCCTCATCCAACACCAACA CGTGACGATA 24816 477 2.47e-05 CCACGTGTAT TCCATCCCATCACTTCTCCA TCGG 4767 42 2.66e-05 ATACGGTTCA TACTACCCTCCAGTCCTCCC TCCGTCATGC 5824 448 3.32e-05 TTTTCCACAC CACCGTCGGCTTCGCTTCCC ATGGCACCCT 10068 409 4.42e-05 ACACACAAGT CAACTCAACGCTCACACAAC AAGCTCACAA 260835 464 5.44e-05 CTTGGAGCAC CAAACTCACCATCTTTTCCC TCAATGGTGT 17966 281 9.17e-05 GAGTGGACAC GACTGTCAACCTCGCCTCAG TCTCTGCGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25025 1e-09 296_[+1]_184 7012 3.9e-08 59_[+1]_421 31014 6.8e-08 455_[+1]_25 1247 7.9e-08 466_[+1]_14 24736 9e-08 478_[+1]_2 8686 2e-07 29_[+1]_451 1921 2e-07 374_[+1]_106 13996 2.9e-07 445_[+1]_35 3926 3.3e-07 453_[+1]_27 37097 5.9e-07 461_[+1]_19 36837 6.6e-07 93_[+1]_387 1981 1e-06 475_[+1]_5 43150 1.3e-06 474_[+1]_6 263515 1.6e-06 480_[+1] 7406 2.1e-06 308_[+1]_172 264746 4.6e-06 439_[+1]_41 10802 5.5e-06 295_[+1]_185 6963 6.6e-06 34_[+1]_446 31912 6.6e-06 209_[+1]_271 36592 7.2e-06 455_[+1]_25 6597 8.6e-06 379_[+1]_101 3797 1.2e-05 448_[+1]_32 10567 1.2e-05 198_[+1]_282 1962 1.7e-05 164_[+1]_316 25677 2.3e-05 416_[+1]_64 24816 2.5e-05 476_[+1]_4 4767 2.7e-05 41_[+1]_439 5824 3.3e-05 447_[+1]_33 10068 4.4e-05 408_[+1]_72 260835 5.4e-05 463_[+1]_17 17966 9.2e-05 280_[+1]_200 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=31 25025 ( 297) CACCTCCGCCCTCTCCTCGC 1 7012 ( 60) GACCACACACATCACATACC 1 31014 ( 456) CACCACCGCCCTCTCACCTA 1 1247 ( 467) CCCTTCCTACCTCACATCCC 1 24736 ( 479) CAACACCTCTCTCTCTTCCC 1 8686 ( 30) CTCATCAGACCTCACATCGC 1 1921 ( 375) CACAAGCCACCCCACATCCC 1 13996 ( 446) CACATCACCTCTCCCATCCA 1 3926 ( 454) CACAGCCCCTCTCTTTTCCC 1 37097 ( 462) CTCCGCAAACCTCCCCTCCC 1 36837 ( 94) CTCCTCCCTCCTCACAAAGC 1 1981 ( 476) CACAGTACACCACACAACCA 1 43150 ( 475) GACCTCCGCCGACTCCCCCA 1 263515 ( 481) AACAACCCACCACACTCACA 1 7406 ( 309) CAACATACACCACTCATAAC 1 264746 ( 440) CCCCCCCCATCACCCATACA 1 10802 ( 296) CATCACCTCCCTCGCTCCGC 1 6963 ( 35) CACCACCGCCACCGCCACGG 1 31912 ( 210) GCCCACCGCTGACACAAACC 1 36592 ( 456) CACCTCCTCCCCCTTCCATC 1 6597 ( 380) CACGTCACACAACACAAAGC 1 3797 ( 449) CCACATCAACATCACCTCTC 1 10567 ( 199) AGCAACCCTCCTCTCTTACC 1 1962 ( 165) GACCACCGATGCCTCCACCG 1 25677 ( 417) GTCCTCATCCAACACCAACA 1 24816 ( 477) TCCATCCCATCACTTCTCCA 1 4767 ( 42) TACTACCCTCCAGTCCTCCC 1 5824 ( 448) CACCGTCGGCTTCGCTTCCC 1 10068 ( 409) CAACTCAACGCTCACACAAC 1 260835 ( 464) CAAACTCACCATCTTTTCCC 1 17966 ( 281) GACTGTCAACCTCGCCTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 17316 bayes= 9.83031 E= 2.7e-013 -197 150 -33 -204 142 -57 -291 -104 -65 175 -1160 -303 20 128 -291 -145 73 -189 -59 42 -1160 169 -291 -45 20 157 -1160 -1160 -65 81 9 -72 84 81 -291 -145 -1160 163 -291 -23 -39 150 -133 -303 35 -89 -1160 105 -1160 201 -291 -1160 61 -131 -91 55 -1160 186 -1160 -104 73 57 -1160 -23 -16 -31 -1160 113 49 143 -1160 -1160 -139 136 -33 -145 3 143 -133 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 31 E= 2.7e-013 0.064516 0.677419 0.193548 0.064516 0.677419 0.161290 0.032258 0.129032 0.161290 0.806452 0.000000 0.032258 0.290323 0.580645 0.032258 0.096774 0.419355 0.064516 0.161290 0.354839 0.000000 0.774194 0.032258 0.193548 0.290323 0.709677 0.000000 0.000000 0.161290 0.419355 0.258065 0.161290 0.451613 0.419355 0.032258 0.096774 0.000000 0.741935 0.032258 0.225806 0.193548 0.677419 0.096774 0.032258 0.322581 0.129032 0.000000 0.548387 0.000000 0.967742 0.032258 0.000000 0.387097 0.096774 0.129032 0.387097 0.000000 0.870968 0.000000 0.129032 0.419355 0.354839 0.000000 0.225806 0.225806 0.193548 0.000000 0.580645 0.354839 0.645161 0.000000 0.000000 0.096774 0.612903 0.193548 0.096774 0.258065 0.645161 0.096774 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CAC[CA][AT]C[CA][CG][AC][CT]C[TA]C[AT]C[ACT][TA][CA]C[CA] -------------------------------------------------------------------------------- Time 11.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 34 llr = 330 E-value = 4.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::41112:2211:4:1423: pos.-specific C :::1111111::122::::: probability G 3715413524219129:746 matrix T 735447545379:36:6134 bits 2.1 1.9 1.7 * * 1.4 * * Relative 1.2 ** * Entropy 1.0 ** ** ** (14.0 bits) 0.8 ** ** *** * 0.6 *** * *** **** * 0.4 ****** * *** ****** 0.2 ********* *** ****** 0.0 -------------------- Multilevel TGTGGTTGTGTTGATGTGGG consensus GTATT GTGT TC A TT sequence A G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 31912 377 6.26e-10 ACCCTAAAGG TGAGTTGGTTTTGATGTGTG CAATGTGATG 4767 358 1.75e-08 TCGTTGCCAG TGTTGTTGTGTTGTGGTGAT ATCTGAATAG 1962 243 6.65e-08 ATGAACATGA TGTGGTTGATGTGTTGTGAG GTGATGAGGT 24816 76 1.79e-07 TGTATCGGTG TGTTGTTTGCTTGGTGTGGT GGTTGTTGTA 31598 59 2.44e-07 GTGCACCCAA TGATGTGCTATTGATGTGTT CGTTGATCTC 5824 271 1.26e-06 GAAGCAAAAA TGTGGTATCTTTGAGGAGAG CTGCCCAGAG 37097 158 1.26e-06 CTATGGACCA TTTGTTCGTCATGATGTGGG GTGTGATGTT 263515 29 1.26e-06 AAACGAAGAA GGAGTTAGAGTTGTTGAAGG CGAAGAAACA 10068 44 1.82e-06 GCAAGATACT TGTCGTGTTGTTGACGAGAT AGATCGAGGG 25677 257 2.91e-06 GCACCAGTGA TGTGTGTTGTGTGGTGTGGG AGCTAAAAAA 1247 226 2.91e-06 GCAATGTAGA GGATGGTGTGTAGTTGTGGG GCGTGATGGG 7012 342 3.26e-06 GTAAAGTATC GTTGTTTGATGTGTGGTGAG GGTCGTCATC 39696 322 3.26e-06 GTTGAGATTG TGATGTTCTGTTCTTGAGTT TGTATTGTAA 1981 259 4.52e-06 AGATCTCGGG TGTGTATGTGTAGCGGTGTG TCGGCTGAGA 13996 361 5.03e-06 ATGCCTCTTC TGTTGGTTTGTTGATGTTAT TTGAATCTTC 10802 111 6.88e-06 GATATAATGT GGATGTCGGTTTGATGAAAT CGTGAGAGCA 31014 211 9.29e-06 GTGGTTGGGA GTTGTTGGTTTGGCCGTGGG GTGTCGTAGG 36592 209 1.02e-05 CGGCCGCGTA GGAGGTGCACATGATGTGTT TTGCAAATAT 260835 362 1.02e-05 TTGATGGATC TGAGCTTGGAATGTTGAATG CTACTGCCGA 268243 17 1.24e-05 GTGGAAAGTA GTTCATTGTGTTGGTGTGTG TTGTGTATGG 36837 190 2.15e-05 GCGGTGGTAG GGTGTTGATATTGCGGAGAG GCGGCGAGCA 17966 234 2.15e-05 TTATCCCCTT TGTTTCATTGTTGACATGGG GTACTGAGAT 4568 54 2.35e-05 TAGAGTCGAT TGAGTTAGGATTGGCGTCGG CTGATGATTT 25025 347 2.56e-05 CGCATCGTCC TTTGGTGTCATTGTGGAAGT CAGCTCGTGA 6597 1 3.03e-05 . TGATCAGTATTTGCCGAGGT GTCACTAAAC 24736 315 3.03e-05 TGTACAATCA TCTGTTTGATTAGTTGAGTT TTGTTAGTAT bd790 6 5.33e-05 GATCG TGATGTGTATATGGCATGGG CAGATTCTGC 10567 16 5.33e-05 GGGCATGCCA TTATCATGTGGTGATGTTGT CAATGATTGA 1921 88 7.76e-05 ATGATTTCAT GGAACTTTGTGTGCCGAGGG GTGGGTTTGA 3926 260 1.45e-04 CTGTGTCCGG TTGGATTCGGTTGTTGTGTA TTTGCATGTA 8686 421 1.54e-04 CCTTTGGCCT TTGTGCCTTCTTCATGTGTG CTATCAACCT 3797 155 1.65e-04 GTGTATCTAG TGGATTAGCCATGCTGAGTG CATGTCGGTT 264746 84 3.19e-04 CTTCATCGTA TTGGTATTGATGGATGAAAT TATGATGTAC 7406 71 3.98e-04 GCCTTATGGC GTATTCAGTGGTCAGGTAAG CCCATGATCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31912 6.3e-10 376_[+2]_104 4767 1.7e-08 357_[+2]_123 1962 6.6e-08 242_[+2]_238 24816 1.8e-07 75_[+2]_405 31598 2.4e-07 58_[+2]_422 5824 1.3e-06 270_[+2]_210 37097 1.3e-06 157_[+2]_323 263515 1.3e-06 28_[+2]_452 10068 1.8e-06 43_[+2]_437 25677 2.9e-06 256_[+2]_224 1247 2.9e-06 225_[+2]_255 7012 3.3e-06 341_[+2]_139 39696 3.3e-06 321_[+2]_159 1981 4.5e-06 258_[+2]_222 13996 5e-06 360_[+2]_120 10802 6.9e-06 110_[+2]_370 31014 9.3e-06 210_[+2]_270 36592 1e-05 208_[+2]_272 260835 1e-05 361_[+2]_119 268243 1.2e-05 16_[+2]_464 36837 2.1e-05 189_[+2]_291 17966 2.1e-05 233_[+2]_247 4568 2.3e-05 53_[+2]_427 25025 2.6e-05 346_[+2]_134 6597 3e-05 [+2]_480 24736 3e-05 314_[+2]_166 bd790 5.3e-05 5_[+2]_475 10567 5.3e-05 15_[+2]_465 1921 7.8e-05 87_[+2]_393 3926 0.00014 259_[+2]_221 8686 0.00015 420_[+2]_60 3797 0.00016 154_[+2]_326 264746 0.00032 83_[+2]_397 7406 0.0004 70_[+2]_410 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=34 31912 ( 377) TGAGTTGGTTTTGATGTGTG 1 4767 ( 358) TGTTGTTGTGTTGTGGTGAT 1 1962 ( 243) TGTGGTTGATGTGTTGTGAG 1 24816 ( 76) TGTTGTTTGCTTGGTGTGGT 1 31598 ( 59) TGATGTGCTATTGATGTGTT 1 5824 ( 271) TGTGGTATCTTTGAGGAGAG 1 37097 ( 158) TTTGTTCGTCATGATGTGGG 1 263515 ( 29) GGAGTTAGAGTTGTTGAAGG 1 10068 ( 44) TGTCGTGTTGTTGACGAGAT 1 25677 ( 257) TGTGTGTTGTGTGGTGTGGG 1 1247 ( 226) GGATGGTGTGTAGTTGTGGG 1 7012 ( 342) GTTGTTTGATGTGTGGTGAG 1 39696 ( 322) TGATGTTCTGTTCTTGAGTT 1 1981 ( 259) TGTGTATGTGTAGCGGTGTG 1 13996 ( 361) TGTTGGTTTGTTGATGTTAT 1 10802 ( 111) GGATGTCGGTTTGATGAAAT 1 31014 ( 211) GTTGTTGGTTTGGCCGTGGG 1 36592 ( 209) GGAGGTGCACATGATGTGTT 1 260835 ( 362) TGAGCTTGGAATGTTGAATG 1 268243 ( 17) GTTCATTGTGTTGGTGTGTG 1 36837 ( 190) GGTGTTGATATTGCGGAGAG 1 17966 ( 234) TGTTTCATTGTTGACATGGG 1 4568 ( 54) TGAGTTAGGATTGGCGTCGG 1 25025 ( 347) TTTGGTGTCATTGTGGAAGT 1 6597 ( 1) TGATCAGTATTTGCCGAGGT 1 24736 ( 315) TCTGTTTGATTAGTTGAGTT 1 bd790 ( 6) TGATGTGTATATGGCATGGG 1 10567 ( 16) TTATCATGTGGTGATGTTGT 1 1921 ( 88) GGAACTTTGTGTGCCGAGGG 1 3926 ( 260) TTGGATTCGGTTGTTGTGTA 1 8686 ( 421) TTGTGCCTTCTTCATGTGTG 1 3797 ( 155) TGGATTAGCCATGCTGAGTG 1 264746 ( 84) TTGGTATTGATGGATGAAAT 1 7406 ( 71) GTATTCAGTGGTCAGGTAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 17316 bayes= 9.05919 E= 4.2e-006 -1173 -1173 28 141 -1173 -302 148 15 70 -1173 -104 83 -210 -202 104 53 -210 -102 76 64 -110 -144 -146 141 -52 -144 13 83 -310 -102 104 41 -30 -144 -4 83 -52 -70 54 29 -78 -1173 -46 135 -152 -1173 -204 169 -1173 -144 191 -1173 59 -44 -72 15 -1173 -22 -24 115 -210 -1173 196 -1173 59 -1173 -1173 122 -52 -302 160 -217 22 -1173 66 29 -310 -1173 128 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 34 E= 4.2e-006 0.000000 0.000000 0.294118 0.705882 0.000000 0.029412 0.676471 0.294118 0.411765 0.000000 0.117647 0.470588 0.058824 0.058824 0.500000 0.382353 0.058824 0.117647 0.411765 0.411765 0.117647 0.088235 0.088235 0.705882 0.176471 0.088235 0.264706 0.470588 0.029412 0.117647 0.500000 0.352941 0.205882 0.088235 0.235294 0.470588 0.176471 0.147059 0.352941 0.323529 0.147059 0.000000 0.176471 0.676471 0.088235 0.000000 0.058824 0.852941 0.000000 0.088235 0.911765 0.000000 0.382353 0.176471 0.147059 0.294118 0.000000 0.205882 0.205882 0.588235 0.058824 0.000000 0.941176 0.000000 0.382353 0.000000 0.000000 0.617647 0.176471 0.029412 0.735294 0.058824 0.294118 0.000000 0.382353 0.323529 0.029412 0.000000 0.588235 0.382353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][GT][TA][GT][GT]T[TG][GT][TGA][GT]TTG[AT][TCG]G[TA]G[GTA][GT] -------------------------------------------------------------------------------- Time 22.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 19 llr = 212 E-value = 5.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 21:7623a134:4518 pos.-specific C 3493:87:96194:61 probability G ::::2:::::5:113: matrix T 551:2::::1:12411 bits 2.1 * 1.9 * * 1.7 * ** * 1.4 * ** * Relative 1.2 * **** * Entropy 1.0 ** **** * * (16.1 bits) 0.8 ** ***** * * 0.6 *********** * * 0.4 ************ *** 0.2 **************** 0.0 ---------------- Multilevel TTCAACCACCGCAACA consensus CC CTAA AA CTG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25025 482 6.33e-08 ACTCGTCGTA CACAACCACCGCAACA ACC 10068 483 1.22e-07 ATTACTACCA TTCCAACACCGCAACA AC 263515 403 1.40e-07 GGTTTCACCC TCCAACCACCGCGTGA ACCGACAAAG 5824 157 4.15e-07 GAGAAGGAGA TTCAACCACTACCACA GTCCATTTAG 3797 233 4.15e-07 CGACGGTGTA TCCAACCAACGCCAGA AGGGATAGTA 10567 430 4.15e-07 AACACATCAG CCCATCAACCACAACA CAGAACCAGT 13996 466 1.79e-06 CTCCCATCCA ATCAACCACCCCCAAA CACATAGGCA 39696 11 1.97e-06 CCGCGCGTGT CCTCACCACCGCCTCA CGACGTGCAC 36837 485 1.97e-06 ACGCCAACCA ATCATCCACCGTCACA 36592 401 1.97e-06 TTGCTTGTGC TTCATACACAGCATGA TGTCCCACAC 24736 462 3.47e-06 CAGCAGCTTC TTCAGCAACAGCAGCA ACAACACCTC 1962 393 3.80e-06 AGCCATCTAA CTCAACCACACCCTCC AAATCACAGA 31014 479 7.97e-06 TCACCTACCA TCCCAACACAACAATA TAAACC 17966 316 7.97e-06 GCGGCCGGCC TCCCGACACAACTTCA TATACAACGC 43150 448 1.08e-05 CCGCCCCGCC CCCCACCAACGCGGCA GGCCGTCAAC 31912 7 1.16e-05 CAAGTC ATCAACAACCACTTGT CTAAAATAAC bd790 420 1.43e-05 AATTGGTAGA ATCATCAACCGTTTCA GCAAAGATAT 7012 201 1.63e-05 GGGAGTGTGG CACCACCACCACCAAC AGGGACGAGG 6597 413 1.63e-05 AATGAAGTCA TCCAGCAACAACATGT ACGGATAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25025 6.3e-08 481_[+3]_3 10068 1.2e-07 482_[+3]_2 263515 1.4e-07 402_[+3]_82 5824 4.1e-07 156_[+3]_328 3797 4.1e-07 232_[+3]_252 10567 4.1e-07 429_[+3]_55 13996 1.8e-06 465_[+3]_19 39696 2e-06 10_[+3]_474 36837 2e-06 484_[+3] 36592 2e-06 400_[+3]_84 24736 3.5e-06 461_[+3]_23 1962 3.8e-06 392_[+3]_92 31014 8e-06 478_[+3]_6 17966 8e-06 315_[+3]_169 43150 1.1e-05 447_[+3]_37 31912 1.2e-05 6_[+3]_478 bd790 1.4e-05 419_[+3]_65 7012 1.6e-05 200_[+3]_284 6597 1.6e-05 412_[+3]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=19 25025 ( 482) CACAACCACCGCAACA 1 10068 ( 483) TTCCAACACCGCAACA 1 263515 ( 403) TCCAACCACCGCGTGA 1 5824 ( 157) TTCAACCACTACCACA 1 3797 ( 233) TCCAACCAACGCCAGA 1 10567 ( 430) CCCATCAACCACAACA 1 13996 ( 466) ATCAACCACCCCCAAA 1 39696 ( 11) CCTCACCACCGCCTCA 1 36837 ( 485) ATCATCCACCGTCACA 1 36592 ( 401) TTCATACACAGCATGA 1 24736 ( 462) TTCAGCAACAGCAGCA 1 1962 ( 393) CTCAACCACACCCTCC 1 31014 ( 479) TCCCAACACAACAATA 1 17966 ( 316) TCCCGACACAACTTCA 1 43150 ( 448) CCCCACCAACGCGGCA 1 31912 ( 7) ATCAACAACCACTTGT 1 bd790 ( 420) ATCATCAACCGTTTCA 1 7012 ( 201) CACCACCACCACCAAC 1 6597 ( 413) TCCAGCAACAACATGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 17460 bayes= 10.7404 E= 5.8e-001 -27 40 -1089 84 -126 81 -1089 84 -1089 198 -1089 -233 143 40 -1089 -1089 132 -1089 -62 -33 -27 172 -1089 -1089 6 162 -1089 -1089 198 -1089 -1089 -1089 -126 190 -1089 -1089 32 140 -1089 -233 54 -118 112 -1089 -1089 190 -1089 -133 54 62 -120 -75 90 -1089 -120 67 -126 127 12 -233 164 -118 -1089 -133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 19 E= 5.8e-001 0.210526 0.315789 0.000000 0.473684 0.105263 0.421053 0.000000 0.473684 0.000000 0.947368 0.000000 0.052632 0.684211 0.315789 0.000000 0.000000 0.631579 0.000000 0.157895 0.210526 0.210526 0.789474 0.000000 0.000000 0.263158 0.736842 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.105263 0.894737 0.000000 0.000000 0.315789 0.631579 0.000000 0.052632 0.368421 0.105263 0.526316 0.000000 0.000000 0.894737 0.000000 0.105263 0.368421 0.368421 0.105263 0.157895 0.473684 0.000000 0.105263 0.421053 0.105263 0.578947 0.263158 0.052632 0.789474 0.105263 0.000000 0.105263 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TCA][TC]C[AC][AT][CA][CA]AC[CA][GA]C[AC][AT][CG]A -------------------------------------------------------------------------------- Time 33.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10068 2.56e-07 43_[+2(1.82e-06)]_345_\ [+1(4.42e-05)]_54_[+3(1.22e-07)]_2 10567 4.98e-06 15_[+2(5.33e-05)]_163_\ [+1(1.21e-05)]_211_[+3(4.15e-07)]_55 10802 1.67e-04 110_[+2(6.88e-06)]_165_\ [+1(5.53e-06)]_185 1247 3.59e-06 225_[+2(2.91e-06)]_24_\ [+2(6.21e-05)]_23_[+2(4.93e-05)]_134_[+1(7.86e-08)]_14 13996 7.69e-08 360_[+2(5.03e-06)]_65_\ [+1(2.88e-07)]_[+3(1.79e-06)]_19 17966 1.75e-04 233_[+2(2.15e-05)]_27_\ [+1(9.17e-05)]_15_[+3(7.97e-06)]_12_[+3(7.20e-05)]_141 1921 1.58e-04 87_[+2(7.76e-05)]_267_\ [+1(1.98e-07)]_106 1962 1.19e-07 164_[+1(1.67e-05)]_58_\ [+2(6.65e-08)]_11_[+2(3.58e-05)]_99_[+3(3.80e-06)]_92 1981 5.79e-05 258_[+2(4.52e-06)]_197_\ [+1(1.02e-06)]_5 24736 2.48e-07 314_[+2(3.03e-05)]_127_\ [+3(3.47e-06)]_1_[+1(9.01e-08)]_2 24816 1.09e-04 75_[+2(1.79e-07)]_381_\ [+1(2.47e-05)]_4 25025 8.64e-11 296_[+1(1.04e-09)]_30_\ [+2(2.56e-05)]_115_[+3(6.33e-08)]_3 25677 3.46e-05 256_[+2(2.91e-06)]_140_\ [+1(2.29e-05)]_64 260835 2.51e-03 361_[+2(1.02e-05)]_82_\ [+1(5.44e-05)]_17 263515 9.84e-09 28_[+2(1.26e-06)]_354_\ [+3(1.40e-07)]_62_[+1(1.56e-06)] 264746 4.74e-03 439_[+1(4.60e-06)]_41 268243 5.34e-02 16_[+2(1.24e-05)]_464 31014 1.41e-07 210_[+2(9.29e-06)]_225_\ [+1(6.83e-08)]_3_[+3(7.97e-06)]_6 31598 5.34e-03 58_[+2(2.44e-07)]_422 31912 1.95e-09 6_[+3(1.16e-05)]_187_[+1(6.62e-06)]_\ 147_[+2(6.26e-10)]_104 36592 2.93e-06 208_[+2(1.02e-05)]_172_\ [+3(1.97e-06)]_39_[+1(7.23e-06)]_25 36837 6.59e-07 93_[+1(6.56e-07)]_76_[+2(2.15e-05)]_\ 236_[+1(7.58e-05)]_19_[+3(1.97e-06)] 37097 3.42e-06 157_[+2(1.26e-06)]_14_\ [+2(6.70e-05)]_250_[+1(5.86e-07)]_19 3797 1.32e-05 232_[+3(4.15e-07)]_200_\ [+1(1.21e-05)]_3_[+3(5.71e-05)]_13 3926 6.67e-04 453_[+1(3.25e-07)]_27 39696 5.37e-05 10_[+3(1.97e-06)]_295_\ [+2(3.26e-06)]_159 43150 2.89e-04 399_[+1(3.57e-05)]_16_\ [+1(1.02e-05)]_19_[+1(1.27e-06)]_6 4568 1.75e-01 53_[+2(2.35e-05)]_427 4767 1.54e-05 41_[+1(2.66e-05)]_296_\ [+2(1.75e-08)]_123 5824 4.31e-07 156_[+3(4.15e-07)]_98_\ [+2(1.26e-06)]_157_[+1(3.32e-05)]_33 6597 5.74e-05 [+2(3.03e-05)]_359_[+1(8.61e-06)]_\ 13_[+3(1.63e-05)]_72 6963 1.24e-03 34_[+1(6.62e-06)]_446 7012 6.17e-08 59_[+1(3.86e-08)]_121_\ [+3(1.63e-05)]_125_[+2(3.26e-06)]_139 7406 2.63e-03 212_[+1(1.31e-05)]_76_\ [+1(2.12e-06)]_50_[+1(5.44e-05)]_102 8686 1.13e-04 29_[+1(1.98e-07)]_229_\ [+1(2.12e-05)]_202 bd790 8.16e-03 5_[+2(5.33e-05)]_394_[+3(1.43e-05)]_\ 65 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************