******************************************************************************** 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/225/225.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11179 1.0000 500 17144 1.0000 500 20723 1.0000 500 21265 1.0000 500 21949 1.0000 500 22622 1.0000 500 23408 1.0000 500 24261 1.0000 500 24510 1.0000 500 25031 1.0000 500 33946 1.0000 500 34742 1.0000 500 35239 1.0000 500 36648 1.0000 500 3916 1.0000 500 40010 1.0000 500 40798 1.0000 500 41106 1.0000 500 5106 1.0000 500 6612 1.0000 500 7539 1.0000 500 9831 1.0000 500 bd1811 1.0000 314 ******************************************************************************** ******************************************************************************** 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/225/225.seqs.fa -oc motifs/225 -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= 23 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= 11314 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.243 G 0.232 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.243 G 0.232 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 23 llr = 212 E-value = 2.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2::1:::31:22 pos.-specific C ::::2:::1:3: probability G 71:912a3:924 matrix T :9a:77:48134 bits 2.1 * 1.9 * * 1.7 * * * 1.5 *** * * Relative 1.3 *** * * Entropy 1.1 **** ** ** (13.3 bits) 0.8 **** ** ** 0.6 ******* ** 0.4 ********** * 0.2 ********** * 0.0 ------------ Multilevel GTTGTTGTTGTT consensus A CG A CG sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 23408 293 3.22e-07 TCATGGTTGT GTTGTTGTTGCG AGAAGCGAGA 40010 202 8.24e-07 GAGAGCCGGG GTTGTTGTTGGT GGCAGGACTT 24510 208 1.14e-06 TTGGAAGAGA GTTGTTGGTGAG CAGGCAGGAA 3916 192 2.48e-06 AGAGTTTGTC GTTGCTGATGCT GGTGGGTAGG 25031 111 3.36e-06 AACGATATAG ATTGTTGATGTG GCTGTTTAAA bd1811 200 3.62e-06 CCGAAAATAA GTTGTTGATGGA AAGTGACGCA 6612 61 3.62e-06 GATGTCTGTG GTTGTGGTTGAT GGCTCGAGCA 21949 444 3.62e-06 GAAGTCAGCA GTTGTGGTTGAT ACAGTGTAGT 20723 303 4.17e-06 CTGGTGGTTG ATTGTTGGTGTT AGGTTGTTGT 41106 105 4.66e-06 AACATTTAGA GTTGTTGTAGTT GTATTTCACT 11179 360 9.59e-06 TGCGAAGCAA GTTGTTGAAGAG TTGGAGGCTT 7539 274 1.35e-05 GTGGTGCTGT GGTGTTGTTGAG TCGGCCATTG 34742 187 1.99e-05 GATGGCTGCT GTTGCTGTCGTG CAGGTGGATG 40798 237 2.16e-05 AGTCTATTGA GTTTTTGATGTT CAACCGCTGT 17144 222 2.86e-05 GATGGCATGT GTTGTGGTCGCT TTCAACTCAT 35239 141 3.40e-05 CCCACCTCGT GTTGGGGGTGCT TGGTAATTGG 21265 101 4.65e-05 GAGCTCGAGT GTTGGGGGTGGG CGAGTTAGTT 24261 128 8.93e-05 CACTCATTTT GTTATTGTTTTG GAGAATTGAC 22622 361 1.16e-04 GACGATTAGA GTTGCAGGTGTA ACCAGCCAAC 33946 428 1.32e-04 CAACAGTAAT ATTGATGGTGTA AGAGATCACA 36648 361 1.91e-04 TATTGTTCAC ATTATTGAAGCG TATGAGTACA 9831 370 2.38e-04 TGAACCATCC AGTGCTGATGGA AACAAATGTC 5106 290 3.07e-04 ATTCGTCCTG TTTGCTGATTCT TTGTGCCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23408 3.2e-07 292_[+1]_196 40010 8.2e-07 201_[+1]_287 24510 1.1e-06 207_[+1]_281 3916 2.5e-06 191_[+1]_297 25031 3.4e-06 110_[+1]_378 bd1811 3.6e-06 199_[+1]_103 6612 3.6e-06 60_[+1]_428 21949 3.6e-06 443_[+1]_45 20723 4.2e-06 302_[+1]_186 41106 4.7e-06 104_[+1]_384 11179 9.6e-06 359_[+1]_129 7539 1.4e-05 273_[+1]_215 34742 2e-05 186_[+1]_302 40798 2.2e-05 236_[+1]_252 17144 2.9e-05 221_[+1]_267 35239 3.4e-05 140_[+1]_348 21265 4.6e-05 100_[+1]_388 24261 8.9e-05 127_[+1]_361 22622 0.00012 360_[+1]_128 33946 0.00013 427_[+1]_61 36648 0.00019 360_[+1]_128 9831 0.00024 369_[+1]_119 5106 0.00031 289_[+1]_199 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=23 23408 ( 293) GTTGTTGTTGCG 1 40010 ( 202) GTTGTTGTTGGT 1 24510 ( 208) GTTGTTGGTGAG 1 3916 ( 192) GTTGCTGATGCT 1 25031 ( 111) ATTGTTGATGTG 1 bd1811 ( 200) GTTGTTGATGGA 1 6612 ( 61) GTTGTGGTTGAT 1 21949 ( 444) GTTGTGGTTGAT 1 20723 ( 303) ATTGTTGGTGTT 1 41106 ( 105) GTTGTTGTAGTT 1 11179 ( 360) GTTGTTGAAGAG 1 7539 ( 274) GGTGTTGTTGAG 1 34742 ( 187) GTTGCTGTCGTG 1 40798 ( 237) GTTTTTGATGTT 1 17144 ( 222) GTTGTGGTCGCT 1 35239 ( 141) GTTGGGGGTGCT 1 21265 ( 101) GTTGGGGGTGGG 1 24261 ( 128) GTTATTGTTTTG 1 22622 ( 361) GTTGCAGGTGTA 1 33946 ( 428) ATTGATGGTGTA 1 36648 ( 361) ATTATTGAAGCG 1 9831 ( 370) AGTGCTGATGGA 1 5106 ( 290) TTTGCTGATTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11061 bayes= 8.90663 E= 2.4e-007 -30 -1117 167 -256 -1117 -1117 -142 183 -1117 -1117 -1117 196 -162 -1117 190 -256 -262 -16 -142 134 -262 -1117 -10 152 -1117 -1117 210 -1117 38 -1117 17 60 -103 -148 -1117 160 -1117 -1117 197 -157 -30 10 -42 43 -62 -1117 75 76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 23 E= 2.4e-007 0.217391 0.000000 0.739130 0.043478 0.000000 0.000000 0.086957 0.913043 0.000000 0.000000 0.000000 1.000000 0.086957 0.000000 0.869565 0.043478 0.043478 0.217391 0.086957 0.652174 0.043478 0.000000 0.217391 0.739130 0.000000 0.000000 1.000000 0.000000 0.347826 0.000000 0.260870 0.391304 0.130435 0.086957 0.000000 0.782609 0.000000 0.000000 0.913043 0.086957 0.217391 0.260870 0.173913 0.347826 0.173913 0.000000 0.391304 0.434783 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA]TTG[TC][TG]G[TAG]TG[TCA][TG] -------------------------------------------------------------------------------- Time 5.72 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 23 llr = 245 E-value = 3.0e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:2::51::1::113:121: pos.-specific C 68229:354:a::8473383 probability G ::311:123::32::132:1 matrix T 3247:45339:671223215 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 CCTTCATCCTCTTCCCCCCT consensus T G TCTG GG A GA C sequence GT TG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 20723 470 1.37e-09 CTCACGCCCT CCTTCATTTTCTTCCCGTCT ACCCATCAAA 21265 289 3.94e-08 TCCTTTGCCT CCCTCAACCTCTTCCCTCCC CTTGAGCAAA 5106 445 6.24e-08 CATCAACTTC CCCCCTCCTTCGTCCCGCCT CGTCAACAGA 34742 97 1.68e-07 TTTTGGTTTG TCATCATCGTCGTCTCCACC GGTGCCATTT 40010 406 8.26e-07 ACATCCCATT CCTTGTTCCTCTTCCTCCCG ATGCCCGCAA 23408 455 1.15e-06 GGCATGTGGA CTATCTCTCTCGTCTCTCCT CATCTCATCA 7539 406 1.28e-06 GCTGTACATA CCCTCACTTTCTTACCTTCC ACGAGGAGAA 21949 377 2.40e-06 GTGAAAGGTG ATTTGTTCTTCTTCCCGCCT TTTTATCGGA 22622 479 2.92e-06 TCTGCCAGTT CCATCATTCTCTTCATCTCA AG 41106 422 3.22e-06 GACACTGAAA ACTTCATCTTCTGCCGGACC GCGGGTACAT 11179 464 4.28e-06 GTCCTCTCTC CCTTCCCGCTCGGCTCCGCC TCTCGGCCAT 33946 118 4.70e-06 CACAAACAGT TCGTCATTGTCGTCATCGTT CAAAAAGTCG 3916 154 5.64e-06 CTATTTCAAC TCTGCATCGTCGTATCTACT ACACAGAGAG 24510 179 6.74e-06 ACGCTAGCGT TCGCCATGGTCGACACACCT TGGAAGAGAG 36648 31 7.36e-06 TTCAGAAGCG TCTGCTTTCTCTGCACCGAC ATCACCCGTA 24261 105 1.13e-05 ACGTCCGAAA CCTCCGCGTTCTTCACTCAT TTTGTTATTG 35239 413 1.22e-05 ACACCGTTCT CCGTCTGCGTCTGCCTCGTC GTCGTATCAA 9831 104 1.56e-05 GTGGTGTCCA CCCTCATGCTCAATCCCACT ATTCAACAAG 17144 352 1.56e-05 ACTAGATACT CCAGCATCGACCTCACGGCT CGCTGCAACT bd1811 65 2.65e-05 CCTAACCCTA CTGTCTCCCTCTACAGAACT ACAAAGCAAG 6612 452 2.65e-05 CATTTGCAAG TCGTCTGCCACGTCGCTTCT CCTCTATCGC 25031 449 3.53e-05 CAGGTTGACC CCTTGAACGTCTGTACGTCG TTTCGCGAAG 40798 432 6.42e-05 TCAAGTTACC TTGCCTCGTTCTTTCCGCAC ACGTCTCCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20723 1.4e-09 469_[+2]_11 21265 3.9e-08 288_[+2]_192 5106 6.2e-08 444_[+2]_36 34742 1.7e-07 96_[+2]_384 40010 8.3e-07 405_[+2]_75 23408 1.2e-06 454_[+2]_26 7539 1.3e-06 405_[+2]_75 21949 2.4e-06 376_[+2]_104 22622 2.9e-06 478_[+2]_2 41106 3.2e-06 421_[+2]_59 11179 4.3e-06 463_[+2]_17 33946 4.7e-06 117_[+2]_363 3916 5.6e-06 153_[+2]_327 24510 6.7e-06 178_[+2]_302 36648 7.4e-06 30_[+2]_450 24261 1.1e-05 104_[+2]_376 35239 1.2e-05 412_[+2]_68 9831 1.6e-05 103_[+2]_377 17144 1.6e-05 351_[+2]_129 bd1811 2.6e-05 64_[+2]_230 6612 2.6e-05 451_[+2]_29 25031 3.5e-05 448_[+2]_32 40798 6.4e-05 431_[+2]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=23 20723 ( 470) CCTTCATTTTCTTCCCGTCT 1 21265 ( 289) CCCTCAACCTCTTCCCTCCC 1 5106 ( 445) CCCCCTCCTTCGTCCCGCCT 1 34742 ( 97) TCATCATCGTCGTCTCCACC 1 40010 ( 406) CCTTGTTCCTCTTCCTCCCG 1 23408 ( 455) CTATCTCTCTCGTCTCTCCT 1 7539 ( 406) CCCTCACTTTCTTACCTTCC 1 21949 ( 377) ATTTGTTCTTCTTCCCGCCT 1 22622 ( 479) CCATCATTCTCTTCATCTCA 1 41106 ( 422) ACTTCATCTTCTGCCGGACC 1 11179 ( 464) CCTTCCCGCTCGGCTCCGCC 1 33946 ( 118) TCGTCATTGTCGTCATCGTT 1 3916 ( 154) TCTGCATCGTCGTATCTACT 1 24510 ( 179) TCGCCATGGTCGACACACCT 1 36648 ( 31) TCTGCTTTCTCTGCACCGAC 1 24261 ( 105) CCTCCGCGTTCTTCACTCAT 1 35239 ( 413) CCGTCTGCGTCTGCCTCGTC 1 9831 ( 104) CCCTCATGCTCAATCCCACT 1 17144 ( 352) CCAGCATCGACCTCACGGCT 1 bd1811 ( 65) CTGTCTCCCTCTACAGAACT 1 6612 ( 452) TCGTCTGCCACGTCGCTTCT 1 25031 ( 449) CCTTGAACGTCTGTACGTCG 1 40798 ( 432) TTGCCTCGTTCTTTCCGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 10877 bayes= 9.28567 E= 3.0e-006 -162 133 -1117 24 -1117 177 -1117 -57 -62 -48 17 60 -1117 -48 -83 143 -1117 184 -83 -1117 97 -248 -242 60 -162 33 -142 102 -1117 110 -10 2 -1117 69 39 24 -162 -1117 -1117 183 -1117 204 -1117 -1117 -262 -248 58 113 -103 -1117 -10 134 -162 169 -1117 -98 38 84 -242 -57 -1117 161 -142 -57 -162 52 39 2 -30 52 -10 -24 -103 169 -1117 -157 -262 52 -142 102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 23 E= 3.0e-006 0.086957 0.608696 0.000000 0.304348 0.000000 0.826087 0.000000 0.173913 0.173913 0.173913 0.260870 0.391304 0.000000 0.173913 0.130435 0.695652 0.000000 0.869565 0.130435 0.000000 0.521739 0.043478 0.043478 0.391304 0.086957 0.304348 0.086957 0.521739 0.000000 0.521739 0.217391 0.260870 0.000000 0.391304 0.304348 0.304348 0.086957 0.000000 0.000000 0.913043 0.000000 1.000000 0.000000 0.000000 0.043478 0.043478 0.347826 0.565217 0.130435 0.000000 0.217391 0.652174 0.086957 0.782609 0.000000 0.130435 0.347826 0.434783 0.043478 0.173913 0.000000 0.739130 0.086957 0.173913 0.086957 0.347826 0.304348 0.260870 0.217391 0.347826 0.217391 0.217391 0.130435 0.782609 0.000000 0.086957 0.043478 0.347826 0.086957 0.521739 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]C[TG]TC[AT][TC][CTG][CGT]TC[TG][TG]C[CA]C[CGT][CAGT]C[TC] -------------------------------------------------------------------------------- Time 10.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 14 sites = 23 llr = 211 E-value = 4.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :782532:898:57 pos.-specific C 8::721692:2842 probability G 2::::111:::21: matrix T :31:351::1:::1 bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * ***** Entropy 1.1 * ** ***** (13.3 bits) 0.8 * ** ***** * 0.6 **** ******* 0.4 **** ******** 0.2 ************** 0.0 -------------- Multilevel CAACATCCAAACAA consensus T ATA CGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 9831 38 2.75e-07 AGAGATACAG CAACAACCAAAGAA AGTAAAGAAG 21265 479 5.05e-07 GGACCCCGGT CTACATCCAACCAA ACTTCATA 17144 408 5.05e-07 GAGGGACGAA GAACTTCCAAACCA TTTCTTTTAT bd1811 154 1.53e-06 TCATGCATAG CATCCTCCAAACAA CAGGCAATCA 36648 121 2.05e-06 GAGCAGCTCG CAACATGCCAACAA CTACCTCGGC 35239 211 2.60e-06 CACCACTGAC CAAAAAACAAACCA CAGCCACACT 41106 454 2.95e-06 GGGTACATCA CAACTTGCAAACCC TCCTCGTCTT 40798 466 4.12e-06 CTCCCCTACC CTACCACCAAACAC AGCTCCTCTG 34742 463 6.48e-06 AGACGACAGC CCACACCCAAACCA ACCTGTCAAC 24510 95 1.12e-05 ACCACCAACA CTAATTCCAAACCT TCACCACCAG 23408 204 1.37e-05 AGAGATGAAA GAACTTACAAAGAA GCCGCAGCCC 22622 133 1.99e-05 TTGTTCGCAT CAACTACCATACGA ATAAGAAGTG 5106 473 2.61e-05 CTCGTCAACA GAACCCCCCAACCA ACTCTACCAA 7539 108 3.40e-05 CAGCCCGTCT CAACTTCGCACCCA TCACCTCAGC 3916 354 3.40e-05 ACCGCAAAGC CAAAAGCCAAAGCC CAGCCATCCA 33946 347 4.04e-05 CGTCCACCCT CAACCATCCACCCA CCGCGTCAAA 25031 48 5.15e-05 CTCACAAATT GTTCATCCAAACAT CGTCAGTGTC 40010 444 6.02e-05 AATTGACAAG CGACGCCCAAACAA TACAAGAACT 6612 357 6.50e-05 GTGGCATCCA CATCATTCAAAGGA GAGAGATCTG 21949 161 9.41e-05 ATACACCCCA CTGCTTACAACCAA ACGAGCAGCC 20723 391 1.08e-04 GGTCGGTACT CTAGAGTCAAACAA AACATTAGAT 24261 479 2.34e-04 TCGATGCCAC CAAAAAAGAAAGCC AAAGCAAG 11179 420 3.47e-04 AGTCAATAAA CAAAAAGCATCCAT TCTTGGGCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9831 2.8e-07 37_[+3]_449 21265 5e-07 478_[+3]_8 17144 5e-07 407_[+3]_79 bd1811 1.5e-06 153_[+3]_147 36648 2.1e-06 120_[+3]_366 35239 2.6e-06 210_[+3]_276 41106 3e-06 453_[+3]_33 40798 4.1e-06 465_[+3]_21 34742 6.5e-06 462_[+3]_24 24510 1.1e-05 94_[+3]_392 23408 1.4e-05 203_[+3]_283 22622 2e-05 132_[+3]_354 5106 2.6e-05 472_[+3]_14 7539 3.4e-05 107_[+3]_379 3916 3.4e-05 353_[+3]_133 33946 4e-05 346_[+3]_140 25031 5.1e-05 47_[+3]_439 40010 6e-05 443_[+3]_43 6612 6.5e-05 356_[+3]_130 21949 9.4e-05 160_[+3]_326 20723 0.00011 390_[+3]_96 24261 0.00023 478_[+3]_8 11179 0.00035 419_[+3]_67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=23 9831 ( 38) CAACAACCAAAGAA 1 21265 ( 479) CTACATCCAACCAA 1 17144 ( 408) GAACTTCCAAACCA 1 bd1811 ( 154) CATCCTCCAAACAA 1 36648 ( 121) CAACATGCCAACAA 1 35239 ( 211) CAAAAAACAAACCA 1 41106 ( 454) CAACTTGCAAACCC 1 40798 ( 466) CTACCACCAAACAC 1 34742 ( 463) CCACACCCAAACCA 1 24510 ( 95) CTAATTCCAAACCT 1 23408 ( 204) GAACTTACAAAGAA 1 22622 ( 133) CAACTACCATACGA 1 5106 ( 473) GAACCCCCCAACCA 1 7539 ( 108) CAACTTCGCACCCA 1 3916 ( 354) CAAAAGCCAAAGCC 1 33946 ( 347) CAACCATCCACCCA 1 25031 ( 48) GTTCATCCAAACAT 1 40010 ( 444) CGACGCCCAAACAA 1 6612 ( 357) CATCATTCAAAGGA 1 21949 ( 161) CTGCTTACAACCAA 1 20723 ( 391) CTAGAGTCAAACAA 1 24261 ( 479) CAAAAAAGAAAGCC 1 11179 ( 420) CAAAAAGCATCCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 11015 bayes= 9.30389 E= 4.8e-003 -1117 177 -42 -1117 129 -248 -242 2 163 -1117 -242 -98 -30 161 -242 -1117 84 -48 -242 24 19 -90 -142 89 -62 122 -83 -98 -1117 191 -142 -1117 163 -48 -1117 -1117 177 -1117 -1117 -157 155 -16 -1117 -1117 -1117 169 -10 -1117 84 84 -142 -1117 138 -48 -1117 -98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 23 E= 4.8e-003 0.000000 0.826087 0.173913 0.000000 0.652174 0.043478 0.043478 0.260870 0.826087 0.000000 0.043478 0.130435 0.217391 0.739130 0.043478 0.000000 0.478261 0.173913 0.043478 0.304348 0.304348 0.130435 0.086957 0.478261 0.173913 0.565217 0.130435 0.130435 0.000000 0.913043 0.086957 0.000000 0.826087 0.173913 0.000000 0.000000 0.913043 0.000000 0.000000 0.086957 0.782609 0.217391 0.000000 0.000000 0.000000 0.782609 0.217391 0.000000 0.478261 0.434783 0.086957 0.000000 0.695652 0.173913 0.000000 0.130435 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AT]A[CA][AT][TA]CCAA[AC][CG][AC]A -------------------------------------------------------------------------------- Time 15.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11179 1.56e-04 359_[+1(9.59e-06)]_92_\ [+2(4.28e-06)]_17 17144 4.36e-06 221_[+1(2.86e-05)]_118_\ [+2(1.56e-05)]_36_[+3(5.05e-07)]_79 20723 2.06e-08 302_[+1(4.17e-06)]_155_\ [+2(1.37e-09)]_11 21265 3.02e-08 100_[+1(4.65e-05)]_176_\ [+2(3.94e-08)]_170_[+3(5.05e-07)]_8 21949 1.36e-05 160_[+3(9.41e-05)]_202_\ [+2(2.40e-06)]_47_[+1(3.62e-06)]_45 22622 8.57e-05 132_[+3(1.99e-05)]_293_\ [+2(2.29e-05)]_19_[+2(2.92e-06)]_2 23408 1.44e-07 144_[+2(4.33e-05)]_39_\ [+3(1.37e-05)]_75_[+1(3.22e-07)]_150_[+2(1.15e-06)]_26 24261 1.69e-03 104_[+2(1.13e-05)]_3_[+1(8.93e-05)]_\ 361 24510 1.86e-06 37_[+1(2.16e-05)]_45_[+3(1.12e-05)]_\ 70_[+2(6.74e-06)]_9_[+1(1.14e-06)]_281 25031 7.92e-05 47_[+3(5.15e-05)]_49_[+1(3.36e-06)]_\ 326_[+2(3.53e-05)]_32 33946 2.63e-04 117_[+2(4.70e-06)]_209_\ [+3(4.04e-05)]_140 34742 5.35e-07 96_[+2(1.68e-07)]_70_[+1(1.99e-05)]_\ 264_[+3(6.48e-06)]_24 35239 1.76e-05 140_[+1(3.40e-05)]_58_\ [+3(2.60e-06)]_188_[+2(1.22e-05)]_68 36648 4.02e-05 30_[+2(7.36e-06)]_70_[+3(2.05e-06)]_\ 366 3916 8.50e-06 153_[+2(5.64e-06)]_18_\ [+1(2.48e-06)]_150_[+3(3.40e-05)]_133 40010 9.46e-07 184_[+1(3.40e-05)]_5_[+1(8.24e-07)]_\ 192_[+2(8.26e-07)]_18_[+3(6.02e-05)]_43 40798 7.49e-05 236_[+1(2.16e-05)]_183_\ [+2(6.42e-05)]_14_[+3(4.12e-06)]_21 41106 1.02e-06 104_[+1(4.66e-06)]_305_\ [+2(3.22e-06)]_12_[+3(2.95e-06)]_33 5106 8.36e-06 444_[+2(6.24e-08)]_8_[+3(2.61e-05)]_\ 14 6612 8.08e-05 60_[+1(3.62e-06)]_284_\ [+3(6.50e-05)]_81_[+2(2.65e-05)]_29 7539 1.03e-05 21_[+2(2.65e-05)]_66_[+3(3.40e-05)]_\ 152_[+1(1.35e-05)]_120_[+2(1.28e-06)]_75 9831 1.60e-05 37_[+3(2.75e-07)]_52_[+2(1.56e-05)]_\ 377 bd1811 8.17e-07 64_[+2(2.65e-05)]_69_[+3(1.53e-06)]_\ 32_[+1(3.62e-06)]_103 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************