******************************************************************************** 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/106/106.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42547 1.0000 500 42672 1.0000 500 46364 1.0000 500 47831 1.0000 500 47846 1.0000 500 14762 1.0000 500 54872 1.0000 500 48227 1.0000 500 43611 1.0000 500 25417 1.0000 500 49494 1.0000 500 44171 1.0000 500 33757 1.0000 500 10862 1.0000 500 26290 1.0000 500 26432 1.0000 500 54355 1.0000 500 19708 1.0000 500 45894 1.0000 500 43127 1.0000 500 54686 1.0000 500 49103 1.0000 500 46089 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/106/106.seqs.fa -oc motifs/106 -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= 11500 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.251 G 0.230 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.251 G 0.230 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 23 llr = 204 E-value = 1.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 31:::::::31: pos.-specific C :3:7:::6441: probability G 223:a:::313: matrix T 5373:aa4225a bits 2.1 * 1.9 *** * 1.7 *** * 1.5 *** * Relative 1.3 * *** * Entropy 1.1 ****** * (12.8 bits) 0.8 ****** * 0.6 ****** * 0.4 ******* ** 0.2 * ********** 0.0 ------------ Multilevel TCTCGTTCCCTT consensus ATGT TGAG sequence GG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 54872 455 5.99e-07 CACAAAGGAT TCTCGTTTCCTT ACCCTCCAAA 48227 201 1.57e-06 ATTGCTTCGT TCTCGTTCTCTT GACCTTTCTA 10862 135 2.53e-06 AACAAGGAAG TTTCGTTTGCGT TGTTTTCCTT 42547 458 3.90e-06 AATAGGTTTG TCTTGTTCCCTT TACGTGTTTT 54686 155 6.13e-06 GTACAGACGA TTGCGTTCGCTT TTGGATCTTT 43127 391 1.19e-05 CTTCCCCGTC ATTCGTTCGAGT CTCGATCATC 46089 347 1.92e-05 GGTGTTGCCC GATCGTTCGCTT CACTATCAAC 47846 398 1.92e-05 ACAACCAAGT ATTCGTTCCTGT AAAATCTTCG 49103 104 2.18e-05 CTGCAGTCGA TCGCGTTTCATT AGTCGGCACT 14762 456 2.45e-05 TGTCGCTATC GCTCGTTTCTTT TCGACTGCTG 45894 1 2.77e-05 . AGTCGTTTGATT ACATTGATGA 47831 204 2.77e-05 ATAAAAAGTG TGTCGTTTCGGT ATTCAACAAG 44171 27 4.01e-05 TTGTAATTGG AGTTGTTCGCGT ATCGAAGCTT 19708 351 4.82e-05 ATAATAATAA TGTCGTTTCCAT AATTACTGGG 43611 310 5.89e-05 GATTCGTTTT TGGCGTTTTCGT CTTCCGCATA 25417 141 6.51e-05 AACTCTTTCA TATTGTTCCAGT CGGAGAGCTC 54355 435 7.62e-05 TTTTACAGCT GCTCGTTCGAAT AAGTCCTTGT 33757 418 8.18e-05 TGCGAAGTAA TTGTGTTCCTTT GCATTCCTAC 42672 276 8.84e-05 AAAACAGCGA AAGCGTTCCATT CGGCTAACAA 26290 145 9.57e-05 CGCGGCATCG ACGCGTTCGCCT CGCCGCAATG 49494 481 1.32e-04 GACTTGTCCC GTTTGTTCTGTT CTAGAGAG 46364 301 1.64e-04 CCGAATTGTA CCTCGTTCTTGT TGCCGCATCC 26432 270 2.95e-04 GAAAAATGAA GTTTGTTTTGCT GTTGTCTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54872 6e-07 454_[+1]_34 48227 1.6e-06 200_[+1]_288 10862 2.5e-06 134_[+1]_354 42547 3.9e-06 457_[+1]_31 54686 6.1e-06 154_[+1]_334 43127 1.2e-05 390_[+1]_98 46089 1.9e-05 346_[+1]_142 47846 1.9e-05 397_[+1]_91 49103 2.2e-05 103_[+1]_385 14762 2.4e-05 455_[+1]_33 45894 2.8e-05 [+1]_488 47831 2.8e-05 203_[+1]_285 44171 4e-05 26_[+1]_462 19708 4.8e-05 350_[+1]_138 43611 5.9e-05 309_[+1]_179 25417 6.5e-05 140_[+1]_348 54355 7.6e-05 434_[+1]_54 33757 8.2e-05 417_[+1]_71 42672 8.8e-05 275_[+1]_213 26290 9.6e-05 144_[+1]_344 49494 0.00013 480_[+1]_8 46364 0.00016 300_[+1]_188 26432 0.00029 269_[+1]_219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=23 54872 ( 455) TCTCGTTTCCTT 1 48227 ( 201) TCTCGTTCTCTT 1 10862 ( 135) TTTCGTTTGCGT 1 42547 ( 458) TCTTGTTCCCTT 1 54686 ( 155) TTGCGTTCGCTT 1 43127 ( 391) ATTCGTTCGAGT 1 46089 ( 347) GATCGTTCGCTT 1 47846 ( 398) ATTCGTTCCTGT 1 49103 ( 104) TCGCGTTTCATT 1 14762 ( 456) GCTCGTTTCTTT 1 45894 ( 1) AGTCGTTTGATT 1 47831 ( 204) TGTCGTTTCGGT 1 44171 ( 27) AGTTGTTCGCGT 1 19708 ( 351) TGTCGTTTCCAT 1 43611 ( 310) TGGCGTTTTCGT 1 25417 ( 141) TATTGTTCCAGT 1 54355 ( 435) GCTCGTTCGAAT 1 33757 ( 418) TTGTGTTCCTTT 1 42672 ( 276) AAGCGTTCCATT 1 26290 ( 145) ACGCGTTCGCCT 1 49494 ( 481) GTTTGTTCTGTT 1 46364 ( 301) CCTCGTTCTTGT 1 26432 ( 270) GTTTGTTTTGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 8.93074 E= 1.6e-004 -2 -252 -8 90 -102 47 -8 25 -1117 -1117 18 153 -1117 156 -1117 3 -1117 -1117 212 -1117 -1117 -1117 -1117 197 -1117 -1117 -1117 197 -1117 128 -1117 61 -1117 79 60 -23 -2 79 -82 -55 -160 -153 60 90 -1117 -1117 -1117 197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 23 E= 1.6e-004 0.260870 0.043478 0.217391 0.478261 0.130435 0.347826 0.217391 0.304348 0.000000 0.000000 0.260870 0.739130 0.000000 0.739130 0.000000 0.260870 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.608696 0.000000 0.391304 0.000000 0.434783 0.347826 0.217391 0.260870 0.434783 0.130435 0.173913 0.086957 0.086957 0.347826 0.478261 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TAG][CTG][TG][CT]GTT[CT][CGT][CA][TG]T -------------------------------------------------------------------------------- Time 6.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 16 llr = 197 E-value = 2.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::1:::231::::31634143 pos.-specific C 211:361:3:2814123:657 probability G 3:::3322::81444134:1: matrix T 598a52657a:16:51133:: bits 2.1 1.9 * * 1.7 * * * 1.5 * * ** Relative 1.3 * * ** Entropy 1.1 *** *** * (17.8 bits) 0.8 *** ***** * 0.6 **** * ***** *** 0.4 **************** **** 0.2 ********************* 0.0 --------------------- Multilevel TTTTTCTTTTGCTCTAAACCC consensus G CG AC GGG CGTAA sequence G A GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46089 395 1.02e-08 TCTGATCTCC TTTTGGTTTTGCTAGACTCAC ATCTGAACTT 14762 39 2.84e-08 TTCGCGGATC TTTTGCGATTGCTCGAAATCC CTCTCCCCCC 54872 238 4.84e-08 GCAGACGACA TTCTTCTGTTGCGGTACTCAC TTTTGTGTTC 48227 413 7.99e-08 CATCGGCTCA TTTTTCTTCTGCCAGAGTCCC AAAGCAGTTG 19708 382 1.28e-07 GTACCGTATA CCTTTCTTTTGCTGGACTCAC AGTTATCCAA 42672 381 1.79e-07 GCCCATGAAA TTTTCTTTTTGCTGGAGGAGC AGGGTTTGTA 26290 311 6.07e-07 CTGCACGGCT GTTTGCAACTGCTGCAGGCAC CCATACACCA 47846 62 8.00e-07 TTCGGAATCG CTTTTGTGTTCCGGTGAACCC CAGCTTGATT 42547 475 9.56e-07 CCCTTTACGT GTTTTCGGTTGCGCGATATCA TAAAA 10862 149 1.35e-06 GTTTGCGTTG TTTTCCTTCTGGTCAAAACCC AGCCCAGCCC 33757 356 1.35e-06 CACTTGCTCA TTTTTTTAATGCGCTCGGCAA ACTGTCACTA 43611 141 1.87e-06 CCATGATACG TTATTCAATTGCTATAAGCGA ATGAGAATTA 25417 447 3.19e-06 TCGACAGCGT GTTTCCTATTCTTCTGGATCC CAAGTCGAAA 26432 39 4.54e-06 AAAGCGGCGA GTCTCGCTTTGCGGTCCGCCA TCCAAATGAA 54686 106 9.76e-06 GAGTCCGTTC GTTTGGATCTGTTCTTCGTCC GTTCTATCAT 49103 468 1.37e-05 GCCACAACGG CTTTTTGTTTCCGATCAAAAA TAGCACGTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46089 1e-08 394_[+2]_85 14762 2.8e-08 38_[+2]_441 54872 4.8e-08 237_[+2]_242 48227 8e-08 412_[+2]_67 19708 1.3e-07 381_[+2]_98 42672 1.8e-07 380_[+2]_99 26290 6.1e-07 310_[+2]_169 47846 8e-07 61_[+2]_418 42547 9.6e-07 474_[+2]_5 10862 1.3e-06 148_[+2]_331 33757 1.3e-06 355_[+2]_124 43611 1.9e-06 140_[+2]_339 25417 3.2e-06 446_[+2]_33 26432 4.5e-06 38_[+2]_441 54686 9.8e-06 105_[+2]_374 49103 1.4e-05 467_[+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=16 46089 ( 395) TTTTGGTTTTGCTAGACTCAC 1 14762 ( 39) TTTTGCGATTGCTCGAAATCC 1 54872 ( 238) TTCTTCTGTTGCGGTACTCAC 1 48227 ( 413) TTTTTCTTCTGCCAGAGTCCC 1 19708 ( 382) CCTTTCTTTTGCTGGACTCAC 1 42672 ( 381) TTTTCTTTTTGCTGGAGGAGC 1 26290 ( 311) GTTTGCAACTGCTGCAGGCAC 1 47846 ( 62) CTTTTGTGTTCCGGTGAACCC 1 42547 ( 475) GTTTTCGGTTGCGCGATATCA 1 10862 ( 149) TTTTCCTTCTGGTCAAAACCC 1 33757 ( 356) TTTTTTTAATGCGCTCGGCAA 1 43611 ( 141) TTATTCAATTGCTATAAGCGA 1 25417 ( 447) GTTTCCTATTCTTCTGGATCC 1 26432 ( 39) GTCTCGCTTTGCGGTCCGCCA 1 54686 ( 106) GTTTGGATCTGTTCTTCGTCC 1 49103 ( 468) CTTTTTGTTTCCGATCAAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 10.7515 E= 2.4e+001 -1064 -42 44 97 -1064 -200 -1064 187 -208 -100 -1064 167 -1064 -1064 -1064 197 -1064 0 12 97 -1064 117 12 -45 -49 -200 -29 114 24 -1064 -29 97 -208 0 -1064 143 -1064 -1064 -1064 197 -1064 -42 182 -1064 -1064 170 -188 -103 -1064 -200 71 114 -8 58 71 -1064 -208 -200 71 97 124 -42 -88 -203 24 32 44 -203 51 -1064 71 -3 -108 132 -1064 -3 51 100 -88 -1064 24 146 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 2.4e+001 0.000000 0.187500 0.312500 0.500000 0.000000 0.062500 0.000000 0.937500 0.062500 0.125000 0.000000 0.812500 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.562500 0.250000 0.187500 0.187500 0.062500 0.187500 0.562500 0.312500 0.000000 0.187500 0.500000 0.062500 0.250000 0.000000 0.687500 0.000000 0.000000 0.000000 1.000000 0.000000 0.187500 0.812500 0.000000 0.000000 0.812500 0.062500 0.125000 0.000000 0.062500 0.375000 0.562500 0.250000 0.375000 0.375000 0.000000 0.062500 0.062500 0.375000 0.500000 0.625000 0.187500 0.125000 0.062500 0.312500 0.312500 0.312500 0.062500 0.375000 0.000000 0.375000 0.250000 0.125000 0.625000 0.000000 0.250000 0.375000 0.500000 0.125000 0.000000 0.312500 0.687500 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG]TTT[TCG][CG]T[TA][TC]TGC[TG][CGA][TG]A[ACG][AGT][CT][CA][CA] -------------------------------------------------------------------------------- Time 11.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 23 llr = 192 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:8a673393:: pos.-specific C 34::4:11:::a probability G 432::365:22: matrix T :3::::::158: bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.3 ** * ** Entropy 1.1 **** * ** (12.0 bits) 0.8 **** * ** 0.6 ******* ** 0.4 ******** ** 0.2 ************ 0.0 ------------ Multilevel GCAAAAGGATTC consensus CGG CGAA A sequence AT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 44171 484 6.44e-08 TTCTCGAATA GCAAAAGGATTC CATGG 43611 293 3.21e-07 ATGGTATGCC CCAAAAGGATTC GTTTTTGGCG 54686 435 1.97e-06 TCGATCACAA GGAACAGGAATC TTACACTAGT 46364 411 4.18e-06 CCGAGAGAGA ATAAAAGGATTC CAACCGTAGC 46089 23 1.04e-05 CGAGTGGAAG GGAACGGAATTC GCCCCGCAAG 54355 482 1.04e-05 TAGCAATACA GCGACAGGAATC CATCAAC 47831 384 1.41e-05 GGCATTTGGT ACAAAAAGAATC CGAAAACAGA 26432 375 2.11e-05 GAGGCGTCGC CGAACGGAATTC TCCCCGAAGG 54872 3 2.38e-05 CA GCAAAAGGAGGC AGCCTTGATG 19708 270 2.69e-05 TGCTTGAATC GTGACAGAATTC TGCTACAGCG 10862 470 5.23e-05 GTGTTCCTTG CTAACAAAAATC TGATTCTCTT 33757 152 5.23e-05 CGCCGGCACG ACAAAAAGATGC GGCAACCGCA 49103 146 7.00e-05 GCTCGCGGTT GCGAAGGCATTC TCGAAAAGAC 42672 291 8.36e-05 TTCCATTCGG CTAACAAAAGTC ATACGGCAAC 43127 194 9.94e-05 AATCACGTAT GCAAAAAAAGGC GGGCATCGGA 45894 181 1.57e-04 TGAACGAGAG TGAAAACGATTC TTGTATCTAC 26290 274 1.68e-04 TTCTTCTACC CGAACGCAAATC AGAACCCGAT 49494 174 2.05e-04 CGACTAGGAA GCGAAAGGAATG AAGAACTCTT 48227 293 2.05e-04 AAAAGCACAC CTAACGAGTTTC GTAATATCGC 14762 153 2.60e-04 CTCCAAAGGA AGAAAACGTATC AAGGGAAGAA 25417 477 3.07e-04 CCAAGTCGAA ATAAAAGCACTC ATCAATAGAA 42547 167 3.07e-04 TTCTTCCGAA CCGAAGGCATGC CCCTTATATT 47846 199 3.24e-04 TGGCTGGCGA GGAACGAATGTC CCGCTATGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44171 6.4e-08 483_[+3]_5 43611 3.2e-07 292_[+3]_196 54686 2e-06 434_[+3]_54 46364 4.2e-06 410_[+3]_78 46089 1e-05 22_[+3]_466 54355 1e-05 481_[+3]_7 47831 1.4e-05 383_[+3]_105 26432 2.1e-05 374_[+3]_114 54872 2.4e-05 2_[+3]_486 19708 2.7e-05 269_[+3]_219 10862 5.2e-05 469_[+3]_19 33757 5.2e-05 151_[+3]_337 49103 7e-05 145_[+3]_343 42672 8.4e-05 290_[+3]_198 43127 9.9e-05 193_[+3]_295 45894 0.00016 180_[+3]_308 26290 0.00017 273_[+3]_215 49494 0.00021 173_[+3]_315 48227 0.00021 292_[+3]_196 14762 0.00026 152_[+3]_336 25417 0.00031 476_[+3]_12 42547 0.00031 166_[+3]_322 47846 0.00032 198_[+3]_290 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=23 44171 ( 484) GCAAAAGGATTC 1 43611 ( 293) CCAAAAGGATTC 1 54686 ( 435) GGAACAGGAATC 1 46364 ( 411) ATAAAAGGATTC 1 46089 ( 23) GGAACGGAATTC 1 54355 ( 482) GCGACAGGAATC 1 47831 ( 384) ACAAAAAGAATC 1 26432 ( 375) CGAACGGAATTC 1 54872 ( 3) GCAAAAGGAGGC 1 19708 ( 270) GTGACAGAATTC 1 10862 ( 470) CTAACAAAAATC 1 33757 ( 152) ACAAAAAGATGC 1 49103 ( 146) GCGAAGGCATTC 1 42672 ( 291) CTAACAAAAGTC 1 43127 ( 194) GCAAAAAAAGGC 1 45894 ( 181) TGAAAACGATTC 1 26290 ( 274) CGAACGCAAATC 1 49494 ( 174) GCGAAAGGAATG 1 48227 ( 293) CTAACGAGTTTC 1 14762 ( 153) AGAAAACGTATC 1 25417 ( 477) ATAAAAGCACTC 1 42547 ( 167) CCGAAGGCATGC 1 47846 ( 199) GGAACGAATGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 9.334 E= 1.0e+002 -28 28 92 -255 -1117 79 41 3 157 -1117 -8 -1117 192 -1117 -1117 -1117 110 79 -1117 -1117 140 -1117 41 -1117 20 -94 130 -1117 40 -94 118 -1117 172 -1117 -1117 -97 20 -252 -40 90 -1117 -1117 -40 169 -1117 193 -240 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 23 E= 1.0e+002 0.217391 0.304348 0.434783 0.043478 0.000000 0.434783 0.304348 0.260870 0.782609 0.000000 0.217391 0.000000 1.000000 0.000000 0.000000 0.000000 0.565217 0.434783 0.000000 0.000000 0.695652 0.000000 0.304348 0.000000 0.304348 0.130435 0.565217 0.000000 0.347826 0.130435 0.521739 0.000000 0.869565 0.000000 0.000000 0.130435 0.304348 0.043478 0.173913 0.478261 0.000000 0.000000 0.173913 0.826087 0.000000 0.956522 0.043478 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GCA][CGT][AG]A[AC][AG][GA][GA]A[TA]TC -------------------------------------------------------------------------------- Time 17.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42547 1.75e-05 457_[+1(3.90e-06)]_5_[+2(9.56e-07)]_\ 5 42672 2.05e-05 275_[+1(8.84e-05)]_3_[+3(8.36e-05)]_\ 78_[+2(1.79e-07)]_99 46364 6.65e-03 410_[+3(4.18e-06)]_78 47831 3.39e-03 203_[+1(2.77e-05)]_168_\ [+3(1.41e-05)]_105 47846 6.31e-05 61_[+2(8.00e-07)]_315_\ [+1(1.92e-05)]_91 14762 3.42e-06 38_[+2(2.84e-08)]_188_\ [+2(6.68e-05)]_187_[+1(2.45e-05)]_33 54872 2.32e-08 2_[+3(2.38e-05)]_223_[+2(4.84e-08)]_\ 196_[+1(5.99e-07)]_34 48227 6.02e-07 200_[+1(1.57e-06)]_147_\ [+1(3.90e-06)]_41_[+2(7.99e-08)]_67 43611 8.30e-07 140_[+2(1.87e-06)]_131_\ [+3(3.21e-07)]_5_[+1(5.89e-05)]_179 25417 5.60e-04 140_[+1(6.51e-05)]_294_\ [+2(3.19e-06)]_33 49494 5.34e-02 500 44171 4.81e-05 26_[+1(4.01e-05)]_445_\ [+3(6.44e-08)]_5 33757 7.49e-05 151_[+3(5.23e-05)]_192_\ [+2(1.35e-06)]_41_[+1(8.18e-05)]_71 10862 3.55e-06 134_[+1(2.53e-06)]_2_[+2(1.35e-06)]_\ 115_[+3(9.14e-05)]_173_[+3(5.23e-05)]_19 26290 1.15e-04 144_[+1(9.57e-05)]_154_\ [+2(6.07e-07)]_169 26432 2.84e-04 38_[+2(4.54e-06)]_315_\ [+3(2.11e-05)]_114 54355 8.24e-03 387_[+3(5.23e-05)]_35_\ [+1(7.62e-05)]_35_[+3(1.04e-05)]_7 19708 3.31e-06 269_[+3(2.69e-05)]_69_\ [+1(4.82e-05)]_19_[+2(1.28e-07)]_98 45894 2.09e-02 [+1(2.77e-05)]_488 43127 6.76e-03 193_[+3(9.94e-05)]_185_\ [+1(1.19e-05)]_98 54686 2.47e-06 105_[+2(9.76e-06)]_28_\ [+1(6.13e-06)]_268_[+3(1.97e-06)]_54 49103 2.30e-04 103_[+1(2.18e-05)]_30_\ [+3(7.00e-05)]_310_[+2(1.37e-05)]_12 46089 6.24e-08 22_[+3(1.04e-05)]_312_\ [+1(1.92e-05)]_36_[+2(1.02e-08)]_85 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************