******************************************************************************** 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/291/291.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10402 1.0000 500 15950 1.0000 500 20637 1.0000 500 21258 1.0000 500 22293 1.0000 500 23655 1.0000 500 24601 1.0000 500 24835 1.0000 500 2573 1.0000 500 26031 1.0000 500 263640 1.0000 500 263726 1.0000 500 264365 1.0000 500 270365 1.0000 500 28350 1.0000 500 29008 1.0000 500 31810 1.0000 500 3304 1.0000 500 39710 1.0000 500 40233 1.0000 500 40771 1.0000 500 42612 1.0000 500 42704 1.0000 500 460 1.0000 500 5487 1.0000 500 8573 1.0000 500 8719 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/291/291.seqs.fa -oc motifs/291 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.244 G 0.239 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.244 G 0.239 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 18 llr = 237 E-value = 4.9e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2::2::::712::11232::1 pos.-specific C ::11:12:11:1::21:12:: probability G 119:726a143337:533638 matrix T 89:7372:2456727234371 bits 2.1 * 1.9 * 1.7 ** * 1.4 ** * Relative 1.2 ** * Entropy 1.0 *** * * ** ** (19.0 bits) 0.8 ****** ** *** ** 0.6 ********* **** *** 0.4 ***************** *** 0.2 ********************* 0.0 --------------------- Multilevel TTGTGTGGATTTTGTGATGTG consensus AT T GGGGTCAGGTG sequence A TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 460 156 4.00e-12 CGTGCGGATC TTGTGTGGATTTTGTGGTGGG GGGAGATGCG 270365 304 5.20e-09 GGTGGTGCCA TTGTTTGGATTTGTTGTAGTG TATGCAGCGT 22293 305 5.20e-09 GGTGGTGCCA TTGTTTGGATTTGTTGTAGTG TATGCAGCGT 39710 190 2.25e-08 GTCCATCATG TTGTGTTGAGTTTGTGTTTGT GTGCCCCCAA 40771 207 5.77e-08 GCTGGTAAGA TTGTGTGGTGTCTGTAGTCTG TGTATCGGGT 8719 306 7.21e-08 CTCATGTTGC TTGTGGGGGATTTGTGAGGTG GTTCTGATGC 24601 177 1.84e-07 TATTTCATGT TTGATTGGACGGTGTATGGTG AGAGAGGAGG 28350 23 2.03e-07 GTTTGTCCTG TTGTGTTGATATTTCGATGTA GAATGATTGC 10402 387 2.46e-07 GATGACGATG ATGTGCGGAGAGTGTTGTTTG CGTGACGGAC 42704 166 2.71e-07 GGGCCGGTGG TTGAGCGGAGGTGGCAATGGG AATATGCTGG 31810 22 7.20e-07 TATGAAGGTG GTGAGGTGTGTTTGTGGTGTG AGGAGATTGT 263640 199 8.50e-07 CCACGGAGGG TGGTGGTGATGGTGTGTGTGG TGTCCACGTT 24835 346 9.22e-07 GACGACTTTT TTGTTTCGAAATGGTTAACTG CTGACAAAAC 20637 144 9.99e-07 GAAAGATCCT TTCTGTGGAGAGTGCAAGTGG AAAGGACAAC 8573 340 3.71e-06 AAACTTGCTA ATGTGTCGATTTGATCAGCTG ATGCCCCTTT 15950 12 3.71e-06 CACGCAGCTG ATGTTTGGCTTTGGCTTGGTA TGAATTGTGG 40233 175 5.46e-06 AGGCCATGGC TTGCTTCGTGGCTTTGGTTTG GTGCGATGAG 3304 89 6.55e-06 GATCTTCAAT TTGAGTGGATGGTGATGCGGT AGATTCAGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 460 4e-12 155_[+1]_324 270365 5.2e-09 303_[+1]_176 22293 5.2e-09 304_[+1]_175 39710 2.2e-08 189_[+1]_290 40771 5.8e-08 206_[+1]_273 8719 7.2e-08 305_[+1]_174 24601 1.8e-07 176_[+1]_303 28350 2e-07 22_[+1]_457 10402 2.5e-07 386_[+1]_93 42704 2.7e-07 165_[+1]_314 31810 7.2e-07 21_[+1]_458 263640 8.5e-07 198_[+1]_281 24835 9.2e-07 345_[+1]_134 20637 1e-06 143_[+1]_336 8573 3.7e-06 339_[+1]_140 15950 3.7e-06 11_[+1]_468 40233 5.5e-06 174_[+1]_305 3304 6.5e-06 88_[+1]_391 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=18 460 ( 156) TTGTGTGGATTTTGTGGTGGG 1 270365 ( 304) TTGTTTGGATTTGTTGTAGTG 1 22293 ( 305) TTGTTTGGATTTGTTGTAGTG 1 39710 ( 190) TTGTGTTGAGTTTGTGTTTGT 1 40771 ( 207) TTGTGTGGTGTCTGTAGTCTG 1 8719 ( 306) TTGTGGGGGATTTGTGAGGTG 1 24601 ( 177) TTGATTGGACGGTGTATGGTG 1 28350 ( 23) TTGTGTTGATATTTCGATGTA 1 10402 ( 387) ATGTGCGGAGAGTGTTGTTTG 1 42704 ( 166) TTGAGCGGAGGTGGCAATGGG 1 31810 ( 22) GTGAGGTGTGTTTGTGGTGTG 1 263640 ( 199) TGGTGGTGATGGTGTGTGTGG 1 24835 ( 346) TTGTTTCGAAATGGTTAACTG 1 20637 ( 144) TTCTGTGGAGAGTGCAAGTGG 1 8573 ( 340) ATGTGTCGATTTGATCAGCTG 1 15950 ( 12) ATGTTTGGCTTTGGCTTGGTA 1 40233 ( 175) TTGCTTCGTGGCTTTGGTTTG 1 3304 ( 89) TTGAGTGGATGGTGATGCGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 9.62433 E= 4.9e-008 -63 -1081 -210 158 -1081 -1081 -210 186 -1081 -213 198 -1081 -22 -213 -1081 148 -1081 -1081 148 36 -1081 -113 -52 148 -1081 -55 136 -22 -1081 -1081 207 -1081 148 -213 -210 -64 -122 -213 70 78 -22 -1081 22 95 -1081 -113 22 124 -1081 -1081 48 136 -221 -1081 160 -22 -221 -13 -1081 148 -22 -213 107 -22 37 -1081 48 36 -63 -213 48 78 -1081 -55 122 10 -1081 -1081 48 136 -122 -1081 170 -122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 4.9e-008 0.166667 0.000000 0.055556 0.777778 0.000000 0.000000 0.055556 0.944444 0.000000 0.055556 0.944444 0.000000 0.222222 0.055556 0.000000 0.722222 0.000000 0.000000 0.666667 0.333333 0.000000 0.111111 0.166667 0.722222 0.000000 0.166667 0.611111 0.222222 0.000000 0.000000 1.000000 0.000000 0.722222 0.055556 0.055556 0.166667 0.111111 0.055556 0.388889 0.444444 0.222222 0.000000 0.277778 0.500000 0.000000 0.111111 0.277778 0.611111 0.000000 0.000000 0.333333 0.666667 0.055556 0.000000 0.722222 0.222222 0.055556 0.222222 0.000000 0.722222 0.222222 0.055556 0.500000 0.222222 0.333333 0.000000 0.333333 0.333333 0.166667 0.055556 0.333333 0.444444 0.000000 0.166667 0.555556 0.277778 0.000000 0.000000 0.333333 0.666667 0.111111 0.000000 0.777778 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTG[TA][GT]T[GT]GA[TG][TGA][TG][TG][GT][TC][GAT][AGT][TG][GT][TG]G -------------------------------------------------------------------------------- Time 6.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 18 llr = 228 E-value = 5.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 536213:213:31::33:284 pos.-specific C 471681853384:a91493:6 probability G :::1:22:6::23::6:152: matrix T 113125:3:4216:113:1:: bits 2.1 * 1.9 * 1.7 ** * 1.4 * * ** * Relative 1.2 * * ** * * Entropy 1.0 * * * ** * ** (18.3 bits) 0.8 * * * * *** * ** 0.6 *** * *** * *** * ** 0.4 ***** ***** ********* 0.2 ********************* 0.0 --------------------- Multilevel ACACCTCCGTCCTCCGCCGAC consensus CATA A TCA AG AA CGA sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 270365 9 1.46e-09 CGGAGCCA TCACCACCGTCATCCGACGAC TCTTGAGCTT 22293 10 1.46e-09 TCGGAGCCA TCACCACCGTCATCCGACGAC TCTTGAGCTT 26031 428 2.97e-09 TGCACCACAA ACTCCTCTCCCGTCCGACGAC GAGCTACTCA 39710 397 4.16e-09 CCCCCGCCTG CCTCCTCCGCTATCCGCCGAC ACCAGACACC 460 372 1.23e-08 AGCAAAAAAT CCACCTCCGACCTCCACCCGA CGCAGACGAC 2573 178 2.30e-07 ATCAAATGAA AACCCTCCGCCATCCGCCAGA TCGCAGAGAC 24601 465 2.82e-07 TCGCCCAGCA ACTCATCTGACAGCCATCGAC CTCACAATAT 15950 265 3.79e-07 ACAACGAGCA ACAACGCTGCCCACCGCCCAA CTCACACCCA 20637 414 4.58e-07 CTTGAAACAG CCTCCTGCCTCCGCCTTCCAA GTCGACGTAG 40771 104 1.79e-06 CGCACGACGA CCTCCACTCATCTCCTTCAAC AAAAAGGATT 8573 462 2.09e-06 TCGCCTCCAA AAACTTGAATCCTCCACCGAA ACCCACAACG 40233 240 2.09e-06 ATCTAATCAA ACAACTCTCTCCGCTCCCGAA GGAGCTTCTT 28350 188 2.61e-06 CCGCTCGTCT CATACACCGACAGCCGACTGC AGACTTATGA 42704 465 3.71e-06 ACAATAAAGA ACAACGCAGTTGGCCATCAAC TCCAATCCAT 31810 420 3.71e-06 AGGCTATCAC AAATCGGCCTCCGCCACCCAA AAAGTGACGG 5487 351 4.85e-06 GGTTTGGTTC CTAGTTCCGACTTCCGACGGC TTCGAAAAAT 264365 422 5.87e-06 CGCGACGTAC ACCGTCCTCTCTTCCGACGAC GCCTGCTACA 42612 400 7.98e-06 TCACGTGCTA CAACCACAACCGTCCGTGCAA AAAGAATCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270365 1.5e-09 8_[+2]_471 22293 1.5e-09 9_[+2]_470 26031 3e-09 427_[+2]_52 39710 4.2e-09 396_[+2]_83 460 1.2e-08 371_[+2]_108 2573 2.3e-07 177_[+2]_302 24601 2.8e-07 464_[+2]_15 15950 3.8e-07 264_[+2]_215 20637 4.6e-07 413_[+2]_66 40771 1.8e-06 103_[+2]_376 8573 2.1e-06 461_[+2]_18 40233 2.1e-06 239_[+2]_240 28350 2.6e-06 187_[+2]_292 42704 3.7e-06 464_[+2]_15 31810 3.7e-06 419_[+2]_60 5487 4.8e-06 350_[+2]_129 264365 5.9e-06 421_[+2]_58 42612 8e-06 399_[+2]_80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=18 270365 ( 9) TCACCACCGTCATCCGACGAC 1 22293 ( 10) TCACCACCGTCATCCGACGAC 1 26031 ( 428) ACTCCTCTCCCGTCCGACGAC 1 39710 ( 397) CCTCCTCCGCTATCCGCCGAC 1 460 ( 372) CCACCTCCGACCTCCACCCGA 1 2573 ( 178) AACCCTCCGCCATCCGCCAGA 1 24601 ( 465) ACTCATCTGACAGCCATCGAC 1 15950 ( 265) ACAACGCTGCCCACCGCCCAA 1 20637 ( 414) CCTCCTGCCTCCGCCTTCCAA 1 40771 ( 104) CCTCCACTCATCTCCTTCAAC 1 8573 ( 462) AAACTTGAATCCTCCACCGAA 1 40233 ( 240) ACAACTCTCTCCGCTCCCGAA 1 28350 ( 188) CATACACCGACAGCCGACTGC 1 42704 ( 465) ACAACGCAGTTGGCCATCAAC 1 31810 ( 420) AAATCGGCCTCCGCCACCCAA 1 5487 ( 351) CTAGTTCCGACTTCCGACGGC 1 264365 ( 422) ACCGTCCTCTCTTCCGACGAC 1 42612 ( 400) CAACCACAACCGTCCGTGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.3387 E= 5.6e-005 95 67 -1081 -122 11 145 -1081 -222 110 -113 -1081 36 -22 132 -110 -222 -221 167 -1081 -64 11 -213 -52 95 -1081 177 -52 -1081 -63 104 -1081 36 -122 45 122 -1081 11 19 -1081 78 -1081 177 -1081 -64 37 67 -52 -122 -221 -1081 48 124 -1081 203 -1081 -1081 -1081 195 -1081 -222 11 -213 122 -122 37 67 -1081 10 -1081 195 -210 -1081 -63 19 107 -222 159 -1081 -10 -1081 78 119 -1081 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 5.6e-005 0.500000 0.388889 0.000000 0.111111 0.277778 0.666667 0.000000 0.055556 0.555556 0.111111 0.000000 0.333333 0.222222 0.611111 0.111111 0.055556 0.055556 0.777778 0.000000 0.166667 0.277778 0.055556 0.166667 0.500000 0.000000 0.833333 0.166667 0.000000 0.166667 0.500000 0.000000 0.333333 0.111111 0.333333 0.555556 0.000000 0.277778 0.277778 0.000000 0.444444 0.000000 0.833333 0.000000 0.166667 0.333333 0.388889 0.166667 0.111111 0.055556 0.000000 0.333333 0.611111 0.000000 1.000000 0.000000 0.000000 0.000000 0.944444 0.000000 0.055556 0.277778 0.055556 0.555556 0.111111 0.333333 0.388889 0.000000 0.277778 0.000000 0.944444 0.055556 0.000000 0.166667 0.277778 0.500000 0.055556 0.777778 0.000000 0.222222 0.000000 0.444444 0.555556 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC][CA][AT][CA]C[TA]C[CT][GC][TAC]C[CA][TG]CC[GA][CAT]C[GC][AG][CA] -------------------------------------------------------------------------------- Time 13.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 26 llr = 234 E-value = 3.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 15938::96:65 pos.-specific C 2::::2::1:22 probability G 741728a:1a22 matrix T :1::::::2::2 bits 2.1 * 1.9 * * 1.7 * * * 1.4 * ** * Relative 1.2 *** ** * Entropy 1.0 ****** * (13.0 bits) 0.8 * ****** * 0.6 ******** ** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel GAAGAGGAAGAA consensus G AG T GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 270365 435 1.00e-06 AGCGCGTTGG GAAAAGGAAGAA TCCATGTTAC 22293 436 1.00e-06 AGCGCGTTGG GAAAAGGAAGAA TCCATGTTAC 42612 127 1.29e-06 GTGTGCAGCT GTAGAGGAAGAA GAAACGAGTG 264365 41 2.26e-06 TCGGTGCTAT GAAAAGGAAGAT ATGAGCTTTC 263726 48 2.26e-06 AGTTGAGCAA GAAGGGGAAGAT TATTTTGGGA 3304 264 5.01e-06 GACGACGCGA CAAGAGGATGAA TTGTCACGGA 29008 17 5.62e-06 GACGACGTGT CGAGAGGAAGCA GCAGGATGCT 21258 89 6.45e-06 CCAAATCGCT GGAGACGAAGAC GGACCACCAT 10402 275 6.45e-06 CCGAAGATTC GAAGACGAAGCA GGCGATAACC 8719 125 8.04e-06 AGATGACTTG GAAGAGGACGAT CGGCGGCTTC 8573 148 1.66e-05 TACGTCTGGT CGAGAGGATGCA CGTGAAACGT 24601 139 1.89e-05 CGTAGGAGGA GGAGAGGAGGGC TGCGATGGCG 26031 202 3.27e-05 GTGAGCTAAA GGAGAGGGTGAA GGGGGGATAA 460 26 4.07e-05 GTGAACCACG AGAGGGGAAGGA GAAGGTCGAT 40233 135 4.07e-05 TTGTTATCGC GTAAAGGATGAT ACAGACACCA 5487 386 4.41e-05 AAAAATCTTG CGAGAGGACGAC CAAGGCGGGG 28350 278 4.41e-05 CAGCAAGAGC GAGGAGGAAGGC ACCGTAAGTG 20637 233 5.41e-05 TATCAGAGGC GGAAGCGAAGGA TTCTATACGT 42704 147 6.25e-05 TATTCAGACT CAAGAGGAGGGG CCGGTGGTTG 40771 10 7.10e-05 GGATGATCG GTGGAGGAAGAG AGCCATCACT 31810 216 8.19e-05 ACGAGAAGTG AAAGGGGATGAT ACCTTCGCGA 2573 11 8.19e-05 GCGGCGAAGG TGAGAGGAAGCG ATCCCGTCAA 15950 113 8.19e-05 ACTTTGTTTG GAAGGAGAAGGA GATGGCGTGA 263640 340 8.77e-05 CACAGGCTAT GGAGAGGTTGAG GTTAGTGGTG 24835 411 1.55e-04 CCACTTAGGG GGAAACGAAAAA CATTGTTTGT 23655 393 2.99e-04 GACATGAAAT GAAAGCGAGGCT CTCACTTCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270365 1e-06 434_[+3]_54 22293 1e-06 435_[+3]_53 42612 1.3e-06 126_[+3]_362 264365 2.3e-06 40_[+3]_448 263726 2.3e-06 47_[+3]_441 3304 5e-06 263_[+3]_225 29008 5.6e-06 16_[+3]_472 21258 6.5e-06 88_[+3]_400 10402 6.5e-06 274_[+3]_214 8719 8e-06 124_[+3]_364 8573 1.7e-05 147_[+3]_341 24601 1.9e-05 138_[+3]_350 26031 3.3e-05 201_[+3]_287 460 4.1e-05 25_[+3]_463 40233 4.1e-05 134_[+3]_354 5487 4.4e-05 385_[+3]_103 28350 4.4e-05 277_[+3]_211 20637 5.4e-05 232_[+3]_256 42704 6.2e-05 146_[+3]_342 40771 7.1e-05 9_[+3]_479 31810 8.2e-05 215_[+3]_273 2573 8.2e-05 10_[+3]_478 15950 8.2e-05 112_[+3]_376 263640 8.8e-05 339_[+3]_149 24835 0.00016 410_[+3]_78 23655 0.0003 392_[+3]_96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=26 270365 ( 435) GAAAAGGAAGAA 1 22293 ( 436) GAAAAGGAAGAA 1 42612 ( 127) GTAGAGGAAGAA 1 264365 ( 41) GAAAAGGAAGAT 1 263726 ( 48) GAAGGGGAAGAT 1 3304 ( 264) CAAGAGGATGAA 1 29008 ( 17) CGAGAGGAAGCA 1 21258 ( 89) GGAGACGAAGAC 1 10402 ( 275) GAAGACGAAGCA 1 8719 ( 125) GAAGAGGACGAT 1 8573 ( 148) CGAGAGGATGCA 1 24601 ( 139) GGAGAGGAGGGC 1 26031 ( 202) GGAGAGGGTGAA 1 460 ( 26) AGAGGGGAAGGA 1 40233 ( 135) GTAAAGGATGAT 1 5487 ( 386) CGAGAGGACGAC 1 28350 ( 278) GAGGAGGAAGGC 1 20637 ( 233) GGAAGCGAAGGA 1 42704 ( 147) CAAGAGGAGGGG 1 40771 ( 10) GTGGAGGAAGAG 1 31810 ( 216) AAAGGGGATGAT 1 2573 ( 11) TGAGAGGAAGCG 1 15950 ( 113) GAAGGAGAAGGA 1 263640 ( 340) GGAGAGGTTGAG 1 24835 ( 411) GGAAACGAAAAA 1 23655 ( 393) GAAAGCGAGGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13203 bayes= 9.51668 E= 3.5e-006 -175 -34 154 -275 84 -1134 83 -117 184 -1134 -163 -1134 6 -1134 161 -1134 157 -1134 -5 -1134 -274 -34 169 -1134 -1134 -1134 207 -1134 184 -1134 -263 -275 116 -166 -105 -17 -274 -1134 201 -1134 116 -34 -5 -1134 84 -66 -63 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 26 E= 3.5e-006 0.076923 0.192308 0.692308 0.038462 0.461538 0.000000 0.423077 0.115385 0.923077 0.000000 0.076923 0.000000 0.269231 0.000000 0.730769 0.000000 0.769231 0.000000 0.230769 0.000000 0.038462 0.192308 0.769231 0.000000 0.000000 0.000000 1.000000 0.000000 0.923077 0.000000 0.038462 0.038462 0.576923 0.076923 0.115385 0.230769 0.038462 0.000000 0.961538 0.000000 0.576923 0.192308 0.230769 0.000000 0.461538 0.153846 0.153846 0.230769 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AG]A[GA][AG]GGA[AT]G[AG][AT] -------------------------------------------------------------------------------- Time 18.93 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10402 3.17e-05 274_[+3(6.45e-06)]_100_\ [+1(2.46e-07)]_23_[+3(2.81e-05)]_58 15950 2.34e-06 11_[+1(3.71e-06)]_80_[+3(8.19e-05)]_\ 140_[+2(3.79e-07)]_215 20637 5.92e-07 143_[+1(9.99e-07)]_68_\ [+3(5.41e-05)]_169_[+2(4.58e-07)]_66 21258 2.96e-03 88_[+3(6.45e-06)]_400 22293 5.45e-13 9_[+2(1.46e-09)]_229_[+1(9.77e-05)]_\ 24_[+1(5.20e-09)]_110_[+3(1.00e-06)]_53 23655 5.22e-01 500 24601 3.16e-08 138_[+3(1.89e-05)]_26_\ [+1(1.84e-07)]_267_[+2(2.82e-07)]_15 24835 1.70e-03 345_[+1(9.22e-07)]_134 2573 1.95e-04 10_[+3(8.19e-05)]_155_\ [+2(2.30e-07)]_12_[+2(7.31e-05)]_269 26031 3.78e-06 201_[+3(3.27e-05)]_214_\ [+2(2.97e-09)]_52 263640 3.88e-04 198_[+1(8.50e-07)]_120_\ [+3(8.77e-05)]_149 263726 5.95e-03 47_[+3(2.26e-06)]_441 264365 1.98e-04 40_[+3(2.26e-06)]_66_[+3(2.29e-05)]_\ 291_[+2(5.87e-06)]_58 270365 5.45e-13 8_[+2(1.46e-09)]_229_[+1(9.77e-05)]_\ 24_[+1(5.20e-09)]_110_[+3(1.00e-06)]_54 28350 5.61e-07 22_[+1(2.03e-07)]_144_\ [+2(2.61e-06)]_69_[+3(4.41e-05)]_211 29008 5.31e-02 16_[+3(5.62e-06)]_472 31810 4.16e-06 21_[+1(7.20e-07)]_173_\ [+3(8.19e-05)]_192_[+2(3.71e-06)]_60 3304 6.13e-04 88_[+1(6.55e-06)]_154_\ [+3(5.01e-06)]_225 39710 5.77e-09 189_[+1(2.25e-08)]_186_\ [+2(4.16e-09)]_83 40233 8.18e-06 134_[+3(4.07e-05)]_28_\ [+1(5.46e-06)]_44_[+2(2.09e-06)]_240 40771 1.96e-07 9_[+3(7.10e-05)]_82_[+2(1.79e-06)]_\ 82_[+1(5.77e-08)]_273 42612 1.52e-04 126_[+3(1.29e-06)]_261_\ [+2(7.98e-06)]_80 42704 1.36e-06 146_[+3(6.25e-05)]_7_[+1(2.71e-07)]_\ 278_[+2(3.71e-06)]_15 460 1.53e-13 25_[+3(4.07e-05)]_118_\ [+1(4.00e-12)]_195_[+2(1.23e-08)]_108 5487 1.93e-03 350_[+2(4.85e-06)]_14_\ [+3(4.41e-05)]_103 8573 2.63e-06 147_[+3(1.66e-05)]_180_\ [+1(3.71e-06)]_101_[+2(2.09e-06)]_18 8719 6.23e-06 53_[+1(5.17e-05)]_50_[+3(8.04e-06)]_\ 89_[+3(8.19e-05)]_68_[+1(7.21e-08)]_174 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************