******************************************************************************** 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/259/259.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10873 1.0000 500 11434 1.0000 500 13920 1.0000 500 14004 1.0000 500 16828 1.0000 500 19743 1.0000 500 19899 1.0000 500 20541 1.0000 500 22477 1.0000 500 23410 1.0000 500 23568 1.0000 500 25727 1.0000 500 261258 1.0000 500 261660 1.0000 500 264323 1.0000 500 264573 1.0000 500 269819 1.0000 500 269843 1.0000 500 29778 1.0000 500 3663 1.0000 500 38258 1.0000 500 4358 1.0000 500 5776 1.0000 500 6294 1.0000 500 6656 1.0000 500 8797 1.0000 500 9591 1.0000 500 bd1133 1.0000 500 bd457 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/259/259.seqs.fa -oc motifs/259 -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= 29 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= 14500 N= 29 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.237 G 0.247 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.237 G 0.247 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 29 llr = 247 E-value = 5.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1:3123:::1:: pos.-specific C :::11:1:::2: probability G 383261::a139 matrix T 6245169a:851 bits 2.1 * 1.9 ** 1.7 *** * 1.5 *** * Relative 1.2 * *** * Entropy 1.0 * **** * (12.3 bits) 0.8 * **** * 0.6 ** ******* 0.4 *** ******** 0.2 ************ 0.0 ------------ Multilevel TGTTGTTTGTTG consensus GTAGAA G sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 261258 348 2.10e-07 TGTAAGCATT TGGTGTTTGTTG TCTGCCTTGA 9591 100 6.92e-07 AGTGCGGACG TGATGTTTGTGG ATGCGTACCA 23410 198 8.29e-07 GGGTTTGTGT TGTTGTTTGTCG GACTCGGTCT 269843 23 1.37e-06 AACGTGCTGT TGATATTTGTTG ATGAACAATT 6294 193 4.21e-06 ACGGGAGATA TGATGATTGTCG TGAGAGCGGA 11434 96 4.84e-06 TTTTGTGATG TGGTTTTTGTTG TCGATCAAAC 38258 215 7.69e-06 CAGCGTTTTC GGTTGGTTGTTG GGTTGGTTGG 261660 299 7.69e-06 GAGTGTCCGG GGTTGATTGTGG AGGATATGGT 23568 50 1.30e-05 ACTGTTGTGG AGTGGTTTGTTG GGTGTTGGGT 22477 200 1.30e-05 GTTATTGGCG TGTGGTTTGATG TATGGGGGTG 25727 311 1.92e-05 TTTTCACAAC TGTCTTTTGTTG TCCCGTCTCA 16828 315 2.95e-05 GTTTTGTTTG TGTGGTTTGAGG AAGGACTGTA bd457 293 3.30e-05 GCTGCTGGCG GTGTATTTGTTG CGAGAGAGGC 269819 63 4.97e-05 GCAAAGACGC TGATGTTTGTCT GCTGCTCCCC 264573 391 4.97e-05 GTGAATGAGC TGTGTGTTGTTG CCGTGATCAA 10873 298 5.91e-05 TATTTTCCCC TGTCGTCTGTTG TGAATTACTC 3663 35 8.47e-05 ATTTAGAAAC GGAGCTTTGTGG AGCCGACGAG 29778 371 8.47e-05 TTCAGTTGAA GTGAGTTTGTGG TTCGTCTCTC 264323 220 9.21e-05 AAAAGCAAGG GGAGCATTGTTG AATGATAGTG 14004 182 1.07e-04 TTTCAACTAG AGATGATTGATG CAATGGATGG 19743 350 1.16e-04 TCGATGTAGG TTATGTCTGTGG TACTGGCAGA 20541 200 1.25e-04 ATTGTTCATG GTTAGATTGTGG TGAAGGGTAA 19899 342 1.25e-04 ATTGCAAAAA TGTAAGTTGTCG TCGTCGAATA 6656 91 1.46e-04 AAATCGTATG GGGCAATTGTCG TTTATGGCAG 4358 316 1.90e-04 CCATCCTCTA AGGAAATTGTTG GTCTCATTTT 13920 274 2.03e-04 GGGTTCGGCG TTAGGTTTGGCG GCTGTTCGGC 5776 41 2.17e-04 GGAGGACAAT GTGTGGTTGATG CACGATGACT 8797 117 2.61e-04 TCCACCGTGT TTGTATTTGGGG TGTCAAAAGA bd1133 209 3.65e-04 ACCATCTTCA TGACTATTGTTT GAACGCATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261258 2.1e-07 347_[+1]_141 9591 6.9e-07 99_[+1]_389 23410 8.3e-07 197_[+1]_291 269843 1.4e-06 22_[+1]_466 6294 4.2e-06 192_[+1]_296 11434 4.8e-06 95_[+1]_393 38258 7.7e-06 214_[+1]_274 261660 7.7e-06 298_[+1]_190 23568 1.3e-05 49_[+1]_439 22477 1.3e-05 199_[+1]_289 25727 1.9e-05 310_[+1]_178 16828 3e-05 314_[+1]_174 bd457 3.3e-05 292_[+1]_196 269819 5e-05 62_[+1]_426 264573 5e-05 390_[+1]_98 10873 5.9e-05 297_[+1]_191 3663 8.5e-05 34_[+1]_454 29778 8.5e-05 370_[+1]_118 264323 9.2e-05 219_[+1]_269 14004 0.00011 181_[+1]_307 19743 0.00012 349_[+1]_139 20541 0.00012 199_[+1]_289 19899 0.00012 341_[+1]_147 6656 0.00015 90_[+1]_398 4358 0.00019 315_[+1]_173 13920 0.0002 273_[+1]_215 5776 0.00022 40_[+1]_448 8797 0.00026 116_[+1]_372 bd1133 0.00037 208_[+1]_280 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=29 261258 ( 348) TGGTGTTTGTTG 1 9591 ( 100) TGATGTTTGTGG 1 23410 ( 198) TGTTGTTTGTCG 1 269843 ( 23) TGATATTTGTTG 1 6294 ( 193) TGATGATTGTCG 1 11434 ( 96) TGGTTTTTGTTG 1 38258 ( 215) GGTTGGTTGTTG 1 261660 ( 299) GGTTGATTGTGG 1 23568 ( 50) AGTGGTTTGTTG 1 22477 ( 200) TGTGGTTTGATG 1 25727 ( 311) TGTCTTTTGTTG 1 16828 ( 315) TGTGGTTTGAGG 1 bd457 ( 293) GTGTATTTGTTG 1 269819 ( 63) TGATGTTTGTCT 1 264573 ( 391) TGTGTGTTGTTG 1 10873 ( 298) TGTCGTCTGTTG 1 3663 ( 35) GGAGCTTTGTGG 1 29778 ( 371) GTGAGTTTGTGG 1 264323 ( 220) GGAGCATTGTTG 1 14004 ( 182) AGATGATTGATG 1 19743 ( 350) TTATGTCTGTGG 1 20541 ( 200) GTTAGATTGTGG 1 19899 ( 342) TGTAAGTTGTCG 1 6656 ( 91) GGGCAATTGTCG 1 4358 ( 316) AGGAAATTGTTG 1 13920 ( 274) TTAGGTTTGGCG 1 5776 ( 41) GTGTGGTTGATG 1 8797 ( 117) TTGTATTTGGGG 1 bd1133 ( 209) TGACTATTGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 14181 bayes= 9.57255 E= 5.1e-005 -133 -1150 33 119 -1150 -1150 162 -9 41 -1150 16 56 -91 -78 -3 91 -33 -178 125 -90 9 -1150 -84 119 -1150 -178 -1150 186 -1150 -1150 -1150 196 -1150 -1150 202 -1150 -91 -1150 -184 163 -1150 -19 16 101 -1150 -1150 192 -190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 29 E= 5.1e-005 0.103448 0.000000 0.310345 0.586207 0.000000 0.000000 0.758621 0.241379 0.344828 0.000000 0.275862 0.379310 0.137931 0.137931 0.241379 0.482759 0.206897 0.068966 0.586207 0.137931 0.275862 0.000000 0.137931 0.586207 0.000000 0.068966 0.000000 0.931034 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.137931 0.000000 0.068966 0.793103 0.000000 0.206897 0.275862 0.517241 0.000000 0.000000 0.931034 0.068966 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][GT][TAG][TG][GA][TA]TTGT[TGC]G -------------------------------------------------------------------------------- Time 6.79 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 29 llr = 287 E-value = 2.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 224:4:834623625654348 pos.-specific C 823617174367:74353351 probability G :2:2411:::::41:1:33:1 matrix T :432121:1:1:::1:::1:1 bits 2.1 1.9 1.7 1.5 * Relative 1.2 * * Entropy 1.0 * * * * * (14.3 bits) 0.8 * *** *** * * 0.6 * * ********* * ** 0.4 * **************** ** 0.2 * ******************* 0.0 --------------------- Multilevel CTACGCACCACCACAAAAGCA consensus GTTAT AACAAG CCCCAA sequence AC GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1133 13 5.14e-09 ACGGCTTAAA CTACGCACAACCACTAAGCCA AGCAGCTCGC 38258 451 5.14e-09 ACGGCTTAAA CTACGCACAACCACTAAGCCA AGCAGCTCGC 23568 474 4.01e-08 TTTCTCAACC CCACACACCACCGCCGCCACA CATACC 8797 399 1.86e-07 CCATTCCTGT CGTCGCACCCCCACCAAAACG TCGACAGCTA 20541 458 2.15e-07 TACCGTAATC CTACACACCACAGAACACAAA CCTCTCCAGC 11434 451 2.47e-07 TCATCATATT CTCTACACTCCAACAACAACA GCATCAGCAG 13920 461 5.47e-07 TCACCTGCGA CGAGACACCCACACAAACTCA TCATCAAAAC 261660 459 8.98e-07 CATCCCCTCC CATTGCACCACCACCCCAAAC GTCAACACCG 4358 461 2.25e-06 GAAGTGCCCT CAACGCACCCTCGCCACAACT TCAACTTTCA bd457 149 2.51e-06 GCTACACGTC CATCACCACAACGCCACGGAA AGCAGACGAC 9591 477 2.51e-06 GCTCTCCTGT ACTCGCAACACCAACCAACCA ACC 19899 199 3.12e-06 GTTCACCTCC ATTGGCTCAACCGCAACAGCA ACAGATGCAA 269843 347 5.21e-06 TCGTTCAACA CAACACACAACCACACACCTC ATGCAAATAC 10873 410 7.00e-06 CGACAAAAAG CTCTGCGACCACGCCAACGAA CGTACACCCT 269819 467 9.31e-06 AATAAGCCCT CATCATCCAACCAGCCACCCA CCGTCACCCA 6656 395 1.12e-05 GTTAGGGATC ATTTGCAAAACAACAACAGAG CATCTCATCC 16828 92 1.34e-05 CGAGGCACAG CTCTGTACTTCAACAAAGGCA CAACTCTTTG 3663 263 1.47e-05 GGGTAGAGGG AGCTACAAAACCACAGACTAA GTTGTCGTAC 6294 9 1.75e-05 AACTGGTC CGTCGTACCATAAGTAACGAA ACACATAGTC 14004 457 1.90e-05 AACACACGAT CACTACACACCCAACTCCAAA ACGAACTCCA 22477 399 2.26e-05 CGTCCGATCC CCCCGCGCCACAGCGCAGCCA CATACTTCGC 19743 270 2.45e-05 GACGGACGGC CGACAGACAAACAACCAAGCC GACGGCGACG 29778 54 2.89e-05 TATTGTGTCT CTCCAGACTACCACAGAGGGA ACTCTGCTTC 23410 477 2.89e-05 CACATTACTA CCAGTCACTCAAGCAACACAA CTC 5776 382 3.39e-05 GCTTCACTCT CGCCCTAAAAAAAGAACAAAA AGGTCCTCTT 264323 106 1.92e-04 TACTTCCAAA CTACCCTACCTCGACGCGGAA TATTCGTACC 261258 205 2.88e-04 ACAAGCTTGT CGACTTCAAAGAGCAACGCAA GAGATTCCTT 264573 17 4.19e-04 AACAGCAACA ACAGGTACAGTCCCAACAGCA AGTTGCTAGT 25727 453 5.38e-04 AACGCCTGCC CTTGCCAACCAAGGACCCTCT ACGCAGTTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1133 5.1e-09 12_[+2]_467 38258 5.1e-09 450_[+2]_29 23568 4e-08 473_[+2]_6 8797 1.9e-07 398_[+2]_81 20541 2.1e-07 457_[+2]_22 11434 2.5e-07 450_[+2]_29 13920 5.5e-07 460_[+2]_19 261660 9e-07 458_[+2]_21 4358 2.3e-06 460_[+2]_19 bd457 2.5e-06 148_[+2]_331 9591 2.5e-06 476_[+2]_3 19899 3.1e-06 198_[+2]_281 269843 5.2e-06 346_[+2]_133 10873 7e-06 409_[+2]_70 269819 9.3e-06 466_[+2]_13 6656 1.1e-05 394_[+2]_85 16828 1.3e-05 91_[+2]_388 3663 1.5e-05 262_[+2]_217 6294 1.7e-05 8_[+2]_471 14004 1.9e-05 456_[+2]_23 22477 2.3e-05 398_[+2]_81 19743 2.5e-05 269_[+2]_210 29778 2.9e-05 53_[+2]_426 23410 2.9e-05 476_[+2]_3 5776 3.4e-05 381_[+2]_98 264323 0.00019 105_[+2]_374 261258 0.00029 204_[+2]_275 264573 0.00042 16_[+2]_463 25727 0.00054 452_[+2]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=29 bd1133 ( 13) CTACGCACAACCACTAAGCCA 1 38258 ( 451) CTACGCACAACCACTAAGCCA 1 23568 ( 474) CCACACACCACCGCCGCCACA 1 8797 ( 399) CGTCGCACCCCCACCAAAACG 1 20541 ( 458) CTACACACCACAGAACACAAA 1 11434 ( 451) CTCTACACTCCAACAACAACA 1 13920 ( 461) CGAGACACCCACACAAACTCA 1 261660 ( 459) CATTGCACCACCACCCCAAAC 1 4358 ( 461) CAACGCACCCTCGCCACAACT 1 bd457 ( 149) CATCACCACAACGCCACGGAA 1 9591 ( 477) ACTCGCAACACCAACCAACCA 1 19899 ( 199) ATTGGCTCAACCGCAACAGCA 1 269843 ( 347) CAACACACAACCACACACCTC 1 10873 ( 410) CTCTGCGACCACGCCAACGAA 1 269819 ( 467) CATCATCCAACCAGCCACCCA 1 6656 ( 395) ATTTGCAAAACAACAACAGAG 1 16828 ( 92) CTCTGTACTTCAACAAAGGCA 1 3663 ( 263) AGCTACAAAACCACAGACTAA 1 6294 ( 9) CGTCGTACCATAAGTAACGAA 1 14004 ( 457) CACTACACACCCAACTCCAAA 1 22477 ( 399) CCCCGCGCCACAGCGCAGCCA 1 19743 ( 270) CGACAGACAAACAACCAAGCC 1 29778 ( 54) CTCCAGACTACCACAGAGGGA 1 23410 ( 477) CCAGTCACTCAAGCAACACAA 1 5776 ( 382) CGCCCTAAAAAAAGAACAAAA 1 264323 ( 106) CTACCCTACCTCGACGCGGAA 1 261258 ( 205) CGACTTCAAAGAGCAACGCAA 1 264573 ( 17) ACAGGTACAGTCCCAACAGCA 1 25727 ( 453) CTTGCCAACCAAGGACCCTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 8.90388 E= 2.6e-002 -59 181 -1150 -1150 -33 -46 -3 56 67 22 -1150 27 -1150 131 -52 -9 55 -119 86 -190 -1150 161 -184 -31 155 -119 -184 -190 26 154 -1150 -1150 67 92 -1150 -90 126 39 -284 -289 -10 131 -284 -90 41 147 -1150 -1150 118 -278 62 -1150 -59 154 -84 -1150 90 68 -284 -131 109 22 -84 -289 100 103 -1150 -1150 55 54 16 -1150 9 22 48 -131 67 113 -284 -289 155 -119 -184 -190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 29 E= 2.6e-002 0.172414 0.827586 0.000000 0.000000 0.206897 0.172414 0.241379 0.379310 0.413793 0.275862 0.000000 0.310345 0.000000 0.586207 0.172414 0.241379 0.379310 0.103448 0.448276 0.068966 0.000000 0.724138 0.068966 0.206897 0.758621 0.103448 0.068966 0.068966 0.310345 0.689655 0.000000 0.000000 0.413793 0.448276 0.000000 0.137931 0.620690 0.310345 0.034483 0.034483 0.241379 0.586207 0.034483 0.137931 0.344828 0.655172 0.000000 0.000000 0.586207 0.034483 0.379310 0.000000 0.172414 0.689655 0.137931 0.000000 0.482759 0.379310 0.034483 0.103448 0.551724 0.275862 0.137931 0.034483 0.517241 0.482759 0.000000 0.000000 0.379310 0.344828 0.275862 0.000000 0.275862 0.275862 0.344828 0.103448 0.413793 0.517241 0.034483 0.034483 0.758621 0.103448 0.068966 0.068966 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TGA][ATC][CT][GA][CT]A[CA][CA][AC][CA][CA][AG]C[AC][AC][AC][ACG][GAC][CA]A -------------------------------------------------------------------------------- Time 13.78 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 5 llr = 88 E-value = 1.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::a::2::::2::2 pos.-specific C :::8:8a::a::82:8 probability G a:a2:::2:::2:84: matrix T :a:::2:6a:a8::6: bits 2.1 * * * * 1.9 *** * * *** 1.7 *** * * *** 1.5 *** * * *** Relative 1.2 ******* ****** * Entropy 1.0 ******* ******** (25.5 bits) 0.8 ******* ******** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GTGCACCTTCTTCGTC consensus G T A GACGA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- bd1133 165 9.74e-10 AACGTCATCG GTGCACCTTCTTCCTC CGTTGCATCT 19899 438 2.40e-09 TTCATTTAGT GTGCATCTTCTTCGTC AGAGGAAACC 23410 264 6.04e-09 TGGGAGTGTG GTGGACCGTCTTCGTC GCCCTGGGGA 6294 234 1.02e-08 GACGATGGGC GTGCACCATCTTCGGA AGAGGCGGTG 261258 27 1.34e-08 AGATTCGTGA GTGCACCTTCTGAGGC ATTTGATAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1133 9.7e-10 164_[+3]_320 19899 2.4e-09 437_[+3]_47 23410 6e-09 263_[+3]_221 6294 1e-08 233_[+3]_251 261258 1.3e-08 26_[+3]_458 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=5 bd1133 ( 165) GTGCACCTTCTTCCTC 1 19899 ( 438) GTGCATCTTCTTCGTC 1 23410 ( 264) GTGGACCGTCTTCGTC 1 6294 ( 234) GTGCACCATCTTCGGA 1 261258 ( 27) GTGCACCTTCTGAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14065 bayes= 11.709 E= 1.7e+001 -897 -897 202 -897 -897 -897 -897 196 -897 -897 202 -897 -897 175 -30 -897 194 -897 -897 -897 -897 175 -897 -36 -897 208 -897 -897 -37 -897 -30 122 -897 -897 -897 196 -897 208 -897 -897 -897 -897 -897 196 -897 -897 -30 164 -37 175 -897 -897 -897 -24 169 -897 -897 -897 70 122 -37 175 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 1.7e+001 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.200000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.800000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.400000 0.600000 0.200000 0.800000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GTG[CG]A[CT]C[TAG]TCT[TG][CA][GC][TG][CA] -------------------------------------------------------------------------------- Time 20.17 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10873 2.74e-03 297_[+1(5.91e-05)]_100_\ [+2(7.00e-06)]_70 11434 8.96e-06 73_[+1(1.30e-05)]_10_[+1(4.84e-06)]_\ 343_[+2(2.47e-07)]_29 13920 7.21e-04 460_[+2(5.47e-07)]_19 14004 2.76e-03 456_[+2(1.90e-05)]_23 16828 3.01e-04 91_[+2(1.34e-05)]_202_\ [+1(2.95e-05)]_79_[+3(7.34e-05)]_79 19743 5.73e-03 269_[+2(2.45e-05)]_210 19899 2.98e-08 198_[+2(3.12e-06)]_91_\ [+3(3.89e-05)]_111_[+3(2.40e-09)]_47 20541 2.53e-04 457_[+2(2.15e-07)]_22 22477 1.62e-03 199_[+1(1.30e-05)]_187_\ [+2(2.26e-05)]_4_[+2(7.72e-05)]_56 23410 5.47e-09 197_[+1(8.29e-07)]_54_\ [+3(6.04e-09)]_197_[+2(2.89e-05)]_3 23568 5.58e-06 49_[+1(1.30e-05)]_412_\ [+2(4.01e-08)]_6 25727 4.73e-02 310_[+1(1.92e-05)]_178 261258 2.53e-08 26_[+3(1.34e-08)]_305_\ [+1(2.10e-07)]_141 261660 9.48e-05 150_[+2(3.13e-05)]_127_\ [+1(7.69e-06)]_148_[+2(8.98e-07)]_21 264323 3.19e-02 219_[+1(9.21e-05)]_269 264573 2.60e-02 390_[+1(4.97e-05)]_98 269819 5.52e-03 62_[+1(4.97e-05)]_392_\ [+2(9.31e-06)]_13 269843 1.31e-04 22_[+1(1.37e-06)]_312_\ [+2(5.21e-06)]_133 29778 1.30e-02 53_[+2(2.89e-05)]_296_\ [+1(8.47e-05)]_118 3663 4.22e-03 34_[+1(8.47e-05)]_216_\ [+2(1.47e-05)]_217 38258 1.29e-06 214_[+1(7.69e-06)]_224_\ [+2(5.14e-09)]_29 4358 9.35e-04 460_[+2(2.25e-06)]_19 5776 3.48e-02 381_[+2(3.39e-05)]_98 6294 2.50e-08 8_[+2(1.75e-05)]_163_[+1(4.21e-06)]_\ 29_[+3(1.02e-08)]_251 6656 1.34e-02 394_[+2(1.12e-05)]_85 8797 2.99e-04 398_[+2(1.86e-07)]_81 9591 4.31e-05 68_[+1(5.52e-06)]_19_[+1(6.92e-07)]_\ 365_[+2(2.51e-06)]_3 bd1133 8.76e-11 12_[+2(5.14e-09)]_131_\ [+3(9.74e-10)]_204_[+2(5.37e-05)]_56_[+2(1.90e-05)]_18 bd457 1.35e-03 148_[+2(2.51e-06)]_123_\ [+1(3.30e-05)]_196 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************