******************************************************************************** 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/413/413.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 37297 1.0000 500 37580 1.0000 500 37761 1.0000 500 38388 1.0000 500 38409 1.0000 500 38462 1.0000 500 48356 1.0000 500 39076 1.0000 500 39129 1.0000 500 39223 1.0000 500 39341 1.0000 500 39762 1.0000 500 39794 1.0000 500 40608 1.0000 500 40611 1.0000 500 40843 1.0000 500 33124 1.0000 500 33729 1.0000 500 35442 1.0000 500 36007 1.0000 500 33184 1.0000 500 48336 1.0000 500 38903 1.0000 500 10286 1.0000 500 31815 1.0000 500 39006 1.0000 500 33569 1.0000 500 48687 1.0000 500 33645 1.0000 500 39222 1.0000 500 41458 1.0000 500 37057 1.0000 500 46978 1.0000 500 52461 1.0000 500 39391 1.0000 500 38408 1.0000 500 40228 1.0000 500 39509 1.0000 500 40645 1.0000 500 39668 1.0000 500 46977 1.0000 500 37061 1.0000 500 40968 1.0000 500 38262 1.0000 500 50211 1.0000 500 41117 1.0000 500 37400 1.0000 500 40570 1.0000 500 37845 1.0000 500 48349 1.0000 500 49959 1.0000 500 37714 1.0000 500 40525 1.0000 500 40625 1.0000 500 41575 1.0000 500 39906 1.0000 500 38074 1.0000 500 35237 1.0000 500 34587 1.0000 500 49705 1.0000 500 39360 1.0000 500 41578 1.0000 500 41582 1.0000 500 38156 1.0000 500 50643 1.0000 500 54907 1.0000 500 39363 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/413/413.seqs.fa -oc motifs/413 -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= 67 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= 33500 N= 67 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.236 G 0.215 T 0.281 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.236 G 0.215 T 0.281 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 26 llr = 401 E-value = 1.1e-042 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :22::::3:::2::5:251:: pos.-specific C a342125111a11a::31128 probability G :::5:82:91:::::a3342: matrix T :6438:36:8:79:5:11462 bits 2.2 * 2.0 * * * 1.8 * * * * * 1.6 * * * * * * Relative 1.3 * * * * ** * * Entropy 1.1 * ** *** ** * * (22.3 bits) 0.9 * ** *** **** * 0.7 * ************* ** 0.4 **************** **** 0.2 ********************* 0.0 --------------------- Multilevel CTCGTGCTGTCTTCAGCAGTC consensus CTT TA T GGTC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46977 228 9.14e-11 TCTTGATCAC CTCGTGCTGTCTTCAGAAGCC AGGAGATACT 39223 187 9.14e-11 TCTTGATCAC CTCGTGCTGTCTTCAGAAGCC AGGAGATACT 39076 185 9.14e-11 TCTTGATCAC CTCGTGCTGTCTTCAGAAGCC AGGAGATACT 39222 188 1.36e-10 TCTTGATCAC CTTGTGCTGTCTTCAGAAGCC AGGAGATACT 33124 188 1.36e-10 TCTTGATCAC CTTGTGCTGTCTTCAGAAGCC AGGAGATACT 50643 63 8.56e-09 CATTTGCATT CATTTGCAGTCATCTGGATTC TGCGGGATCA 49705 64 8.56e-09 CATTTGCATT CATTTGCAGTCATCTGGATTC TGCGGGATCA 46978 82 8.56e-09 CATATGCATT CATTTGCAGTCATCTGGATTC TGCGGGATCA 31815 57 8.56e-09 CATATGCATT CATTTGCAGTCATCTGGATTC TGCGGGATCA 36007 161 1.66e-08 TGCCGAACCC CCCTTGGAGTCTTCAGGGTTT GTCGGCAGGG 38462 150 1.66e-08 TGTCGAGAAC CCCTTGGAGTCTTCAGGGTTT GTCGACAAGT 33645 389 1.85e-08 AGCCTGGAGG CTTGTGTTGGCTCCTGCGGTC CGTGCGGCTT 41575 282 7.64e-08 AAAGTTACCG CTACCGTTGTCTTCAGCATGC TCTAAAACGT 40968 162 7.64e-08 TGCCGAACCC CCCTTGGAGTCTTCAGGGCTT GTCGGCAGGG 38903 162 7.64e-08 TGCCGAAACC CCCTTGGAGTCTTCAGGGCTT GTCGGCAGGG 33729 281 7.64e-08 AAAGTTACCG CTACCGTTGTCTTCAGCATGC TCTAAAACGG 37297 281 7.64e-08 AAAGTTACCG CTACCGTTGTCTTCAGCATGC TCTAACACGT 40611 150 8.32e-08 TGTCGAGAAC CCCTTGGAGTCTTTAGGGTTC GTCGACAAGT 40843 407 9.82e-08 ACGACGACAT CTCGTCCTCTCTTCTGTTGTC TGCCAAACAA 39363 391 1.07e-07 AGCCTGGAGG CTTGTGTCGGCTCCTGCGGTC CGTGCGGCTT 37057 283 1.83e-07 AAAGTTACCG CTACGGTTGTCTTCAGCATGC TCTAAAACGG 39668 392 2.12e-07 AGCCTGGAGG CTTGTGTCGGCTCCTGCGGCC CGGGAGGCTT 39762 480 3.43e-07 CTACCGCTCC CCTGTCCTGCCTTCTGCCATC 40608 407 3.66e-07 ACAACGACAT CTCGTCCTCTCCTCTGTTGTC TGCCAAACAA 38388 407 3.66e-07 ACGACGACAT CTCGTCCTCTCCTCTGTTGTC TGCCAAACAA 37580 480 9.82e-07 CTACCGCTCC CCTGTCCTGCCCTCTGCCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46977 9.1e-11 227_[+1]_252 39223 9.1e-11 186_[+1]_293 39076 9.1e-11 184_[+1]_295 39222 1.4e-10 187_[+1]_292 33124 1.4e-10 187_[+1]_292 50643 8.6e-09 62_[+1]_417 49705 8.6e-09 63_[+1]_416 46978 8.6e-09 81_[+1]_398 31815 8.6e-09 56_[+1]_423 36007 1.7e-08 160_[+1]_319 38462 1.7e-08 149_[+1]_330 33645 1.9e-08 388_[+1]_91 41575 7.6e-08 281_[+1]_198 40968 7.6e-08 161_[+1]_318 38903 7.6e-08 161_[+1]_318 33729 7.6e-08 280_[+1]_199 37297 7.6e-08 280_[+1]_199 40611 8.3e-08 149_[+1]_330 40843 9.8e-08 406_[+1]_73 39363 1.1e-07 390_[+1]_89 37057 1.8e-07 282_[+1]_197 39668 2.1e-07 391_[+1]_88 39762 3.4e-07 479_[+1] 40608 3.7e-07 406_[+1]_73 38388 3.7e-07 406_[+1]_73 37580 9.8e-07 479_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=26 46977 ( 228) CTCGTGCTGTCTTCAGAAGCC 1 39223 ( 187) CTCGTGCTGTCTTCAGAAGCC 1 39076 ( 185) CTCGTGCTGTCTTCAGAAGCC 1 39222 ( 188) CTTGTGCTGTCTTCAGAAGCC 1 33124 ( 188) CTTGTGCTGTCTTCAGAAGCC 1 50643 ( 63) CATTTGCAGTCATCTGGATTC 1 49705 ( 64) CATTTGCAGTCATCTGGATTC 1 46978 ( 82) CATTTGCAGTCATCTGGATTC 1 31815 ( 57) CATTTGCAGTCATCTGGATTC 1 36007 ( 161) CCCTTGGAGTCTTCAGGGTTT 1 38462 ( 150) CCCTTGGAGTCTTCAGGGTTT 1 33645 ( 389) CTTGTGTTGGCTCCTGCGGTC 1 41575 ( 282) CTACCGTTGTCTTCAGCATGC 1 40968 ( 162) CCCTTGGAGTCTTCAGGGCTT 1 38903 ( 162) CCCTTGGAGTCTTCAGGGCTT 1 33729 ( 281) CTACCGTTGTCTTCAGCATGC 1 37297 ( 281) CTACCGTTGTCTTCAGCATGC 1 40611 ( 150) CCCTTGGAGTCTTTAGGGTTC 1 40843 ( 407) CTCGTCCTCTCTTCTGTTGTC 1 39363 ( 391) CTTGTGTCGGCTCCTGCGGTC 1 37057 ( 283) CTACGGTTGTCTTCAGCATGC 1 39668 ( 392) CTTGTGTCGGCTCCTGCGGCC 1 39762 ( 480) CCTGTCCTGCCTTCTGCCATC 1 40608 ( 407) CTCGTCCTCTCCTCTGTTGTC 1 38388 ( 407) CTCGTCCTCTCCTCTGTTGTC 1 37580 ( 480) CCTGTCCTGCCCTCTGCCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 32160 bayes= 10.8022 E= 1.1e-042 -1134 208 -1134 -1134 -80 19 -1134 104 -80 84 -1134 59 -1134 -62 122 30 -1134 -103 -248 159 -1134 -30 191 -1134 -1134 119 -16 -6 37 -162 -1134 104 -1134 -103 204 -1134 -1134 -162 -90 152 -1134 208 -1134 -1134 -80 -103 -1134 138 -1134 -103 -1134 165 -1134 202 -1134 -287 101 -1134 -1134 71 -1134 -1134 222 -1134 -47 55 69 -129 90 -162 52 -129 -180 -162 98 59 -1134 -4 -48 113 -1134 184 -1134 -87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 1.1e-042 0.000000 1.000000 0.000000 0.000000 0.153846 0.269231 0.000000 0.576923 0.153846 0.423077 0.000000 0.423077 0.000000 0.153846 0.500000 0.346154 0.000000 0.115385 0.038462 0.846154 0.000000 0.192308 0.807692 0.000000 0.000000 0.538462 0.192308 0.269231 0.346154 0.076923 0.000000 0.576923 0.000000 0.115385 0.884615 0.000000 0.000000 0.076923 0.115385 0.807692 0.000000 1.000000 0.000000 0.000000 0.153846 0.115385 0.000000 0.730769 0.000000 0.115385 0.000000 0.884615 0.000000 0.961538 0.000000 0.038462 0.538462 0.000000 0.000000 0.461538 0.000000 0.000000 1.000000 0.000000 0.192308 0.346154 0.346154 0.115385 0.500000 0.076923 0.307692 0.115385 0.076923 0.076923 0.423077 0.423077 0.000000 0.230769 0.153846 0.615385 0.000000 0.846154 0.000000 0.153846 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[TC][CT][GT]TG[CT][TA]GTCTTC[AT]G[CG][AG][GT][TC]C -------------------------------------------------------------------------------- Time 34.46 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 33 llr = 432 E-value = 2.8e-034 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 42:81211122143:::::3: pos.-specific C :38:16128::1522:2:1:: probability G 211:3::3:8::12114a:3: matrix T 552252851:8813794:94a bits 2.2 * 2.0 * 1.8 * * 1.6 * * Relative 1.3 * *** * ** * Entropy 1.1 ** **** * ** * (18.9 bits) 0.9 ** * **** ** ** * 0.7 ** ** **** ** ** * 0.4 * ***** ***** ******* 0.2 ************* ******* 0.0 --------------------- Multilevel TTCATCTTCGTTCATTTGTTT consensus AC GA G ATC G A sequence T C C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 31815 15 1.65e-09 TTCATCTGCA TTCATCTGCATTCATTTGTAT TCATATGCAT 46977 174 1.13e-08 TTGTGTGAAA ACCATATTCGTTAGTTCGTAT CTCTTCATTA 39223 133 1.13e-08 TTGTGTGAAA ACCATATTCGTTAGTTCGTAT CTCTTCGTTA 39076 131 1.13e-08 TTGTGTGAAA ACCATATTCGTTAGTTCGTAT CTCTTCGTTA 50643 11 4.36e-08 TTCATCTGCA TTCATCTGCATTCATTTGCAT TCATTTGCAT 49705 12 4.36e-08 TTCATCTGCA TTCATCTGCATTCATTTGCAT TCATTTGCAT 46978 50 4.36e-08 TTCATCTGCA TTCATCTGCATTCATTTGCAT TCATATGCAT 38903 377 5.58e-08 ATGTACCAGT GCTAGCTTCGTTCACTGGTGT AGGGTCATAC 36007 377 5.58e-08 GTGTACCAGT GCTAGCTTCGTTCACTGGTGT AGGGTCATTT 35442 445 5.58e-08 AAATGGCCAT TACATCTCCGATACTTGGTTT GAGTCATGTA 33729 445 5.58e-08 AAATGGCCAT TACATCTCCGATACTTGGTTT GAGTCATGTA 40611 364 5.58e-08 GTGTACCAGT GCTAGCTTCGTTCACTGGTGT AGGGTCATTT 38462 364 5.58e-08 GTGTACCAGT GCTAGCTTCGTTCACTGGTGT AGGGTCATTT 37297 445 5.58e-08 AAATGGCCAT TACATCTCCGATACTTGGTTT GAGTCATATA 39222 134 1.56e-07 TTGTGTGAAA ACCATTTTTGTTAGTTTGTAT CTCTTTGTTA 33124 134 2.39e-07 TTGTGTGAAA ACCATATTTGTTAGTTCGTAT CTCTTTGTTA 40843 307 2.64e-07 ATCGATTTCC ATCATTCGCGTTCTTGCGTTT GTAGAGCTCA 40608 307 2.64e-07 ATCGATTTCC ATCATTCGCGTTCTTGCGTTT GTAGAGCTCA 38388 307 2.64e-07 ATCGATTTCC ATCATTCGCGTTCTTGCGTTT GTAGAGCTCA 34587 465 2.93e-07 GTACCTTTGT TGCTGATTCGTTCTCTTGTTT CCTAGCTGAG 40625 465 2.93e-07 GTACCTTTGT TGCTGATTCGTTCTCTTGTTT CCTAGCTGAG 37057 445 3.57e-07 AAATGGCCAT TACATCTCCAATACTTGGTTT GAGTCATGTA 33645 443 5.76e-07 TTTACTGCTT TTGAATTGCGTTGTTTTGTTT CGTTGTTCTT 40968 377 7.56e-07 GTGTACCAGT GCTAGCTTTGTTCACTGGTGT AGGGTCATAC 39762 396 9.84e-07 CCTGACTTCG ATCTTCATCGTCGTTTTGTGT TCTTCAATAG 41575 445 1.63e-06 AAATGGTCAT TACATCCCCAATACTTGGTTT GAGTCATATA 39363 443 2.23e-06 TTTACTGCTT TTGAATTGCGTTACGTTGTTT CGTTGTTCTT 39668 443 2.23e-06 GTTACTGCTT TTGAATTGCGTTACGTTGTTT CGTTGTTCTC 52461 396 4.96e-06 CTCAACTGTG ATCTCCATCGTCGTTTTGTGT TCTTCAATAG 37580 396 4.96e-06 CCTGACTTCG ATCTCCATCGTCGTTTTGTGT TCATCAATAG 35237 163 8.86e-06 CTTTGGTGAT ATCAGCTAAGTATATTGGTAT CAGATGGTCA 40570 163 8.86e-06 CTTTGGTGAT ATCAGCTAAGTATATTGGTAT CAGATGGTCA 33184 219 8.86e-06 CAAACAAACT TGCAGAAGCCTCCTTTTGTGT TTGTCTATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31815 1.7e-09 14_[+2]_465 46977 1.1e-08 173_[+2]_306 39223 1.1e-08 132_[+2]_347 39076 1.1e-08 130_[+2]_349 50643 4.4e-08 10_[+2]_469 49705 4.4e-08 11_[+2]_468 46978 4.4e-08 49_[+2]_430 38903 5.6e-08 376_[+2]_103 36007 5.6e-08 376_[+2]_103 35442 5.6e-08 444_[+2]_35 33729 5.6e-08 444_[+2]_35 40611 5.6e-08 363_[+2]_116 38462 5.6e-08 363_[+2]_116 37297 5.6e-08 444_[+2]_35 39222 1.6e-07 133_[+2]_346 33124 2.4e-07 133_[+2]_346 40843 2.6e-07 306_[+2]_173 40608 2.6e-07 306_[+2]_173 38388 2.6e-07 306_[+2]_173 34587 2.9e-07 464_[+2]_15 40625 2.9e-07 464_[+2]_15 37057 3.6e-07 444_[+2]_35 33645 5.8e-07 442_[+2]_37 40968 7.6e-07 376_[+2]_103 39762 9.8e-07 395_[+2]_84 41575 1.6e-06 444_[+2]_35 39363 2.2e-06 442_[+2]_37 39668 2.2e-06 442_[+2]_37 52461 5e-06 395_[+2]_84 37580 5e-06 395_[+2]_84 35237 8.9e-06 162_[+2]_317 40570 8.9e-06 162_[+2]_317 33184 8.9e-06 218_[+2]_261 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=33 31815 ( 15) TTCATCTGCATTCATTTGTAT 1 46977 ( 174) ACCATATTCGTTAGTTCGTAT 1 39223 ( 133) ACCATATTCGTTAGTTCGTAT 1 39076 ( 131) ACCATATTCGTTAGTTCGTAT 1 50643 ( 11) TTCATCTGCATTCATTTGCAT 1 49705 ( 12) TTCATCTGCATTCATTTGCAT 1 46978 ( 50) TTCATCTGCATTCATTTGCAT 1 38903 ( 377) GCTAGCTTCGTTCACTGGTGT 1 36007 ( 377) GCTAGCTTCGTTCACTGGTGT 1 35442 ( 445) TACATCTCCGATACTTGGTTT 1 33729 ( 445) TACATCTCCGATACTTGGTTT 1 40611 ( 364) GCTAGCTTCGTTCACTGGTGT 1 38462 ( 364) GCTAGCTTCGTTCACTGGTGT 1 37297 ( 445) TACATCTCCGATACTTGGTTT 1 39222 ( 134) ACCATTTTTGTTAGTTTGTAT 1 33124 ( 134) ACCATATTTGTTAGTTCGTAT 1 40843 ( 307) ATCATTCGCGTTCTTGCGTTT 1 40608 ( 307) ATCATTCGCGTTCTTGCGTTT 1 38388 ( 307) ATCATTCGCGTTCTTGCGTTT 1 34587 ( 465) TGCTGATTCGTTCTCTTGTTT 1 40625 ( 465) TGCTGATTCGTTCTCTTGTTT 1 37057 ( 445) TACATCTCCAATACTTGGTTT 1 33645 ( 443) TTGAATTGCGTTGTTTTGTTT 1 40968 ( 377) GCTAGCTTTGTTCACTGGTGT 1 39762 ( 396) ATCTTCATCGTCGTTTTGTGT 1 41575 ( 445) TACATCCCCAATACTTGGTTT 1 39363 ( 443) TTGAATTGCGTTACGTTGTTT 1 39668 ( 443) TTGAATTGCGTTACGTTGTTT 1 52461 ( 396) ATCTCCATCGTCGTTTTGTGT 1 37580 ( 396) ATCTCCATCGTCGTTTTGTGT 1 35237 ( 163) ATCAGCTAAGTATATTGGTAT 1 40570 ( 163) ATCAGCTAAGTATATTGGTAT 1 33184 ( 219) TGCAGAAGCCTCCTTTTGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 32160 bayes= 9.96255 E= 2.8e-034 56 -1169 -50 69 -82 36 -124 69 -1169 168 -124 -89 167 -1169 -1169 -89 -155 -196 50 95 -33 128 -1169 -41 -114 -96 -1169 143 -214 -64 63 69 -214 184 -1169 -163 -56 -296 187 -1169 -82 -1169 -1169 159 -214 -96 -1169 154 44 94 -83 -221 32 -16 -50 11 -1169 -16 -182 137 -1169 -1169 -124 169 -1169 -16 76 59 -1169 -1169 222 -1169 -1169 -138 -1169 169 32 -1169 34 49 -1169 -1169 -1169 183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 33 E= 2.8e-034 0.393939 0.000000 0.151515 0.454545 0.151515 0.303030 0.090909 0.454545 0.000000 0.757576 0.090909 0.151515 0.848485 0.000000 0.000000 0.151515 0.090909 0.060606 0.303030 0.545455 0.212121 0.575758 0.000000 0.212121 0.121212 0.121212 0.000000 0.757576 0.060606 0.151515 0.333333 0.454545 0.060606 0.848485 0.000000 0.090909 0.181818 0.030303 0.787879 0.000000 0.151515 0.000000 0.000000 0.848485 0.060606 0.121212 0.000000 0.818182 0.363636 0.454545 0.121212 0.060606 0.333333 0.212121 0.151515 0.303030 0.000000 0.212121 0.060606 0.727273 0.000000 0.000000 0.090909 0.909091 0.000000 0.212121 0.363636 0.424242 0.000000 0.000000 1.000000 0.000000 0.000000 0.090909 0.000000 0.909091 0.333333 0.000000 0.272727 0.393939 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA][TC]CA[TG][CAT]T[TG]CGTT[CA][ATC][TC]T[TGC]GT[TAG]T -------------------------------------------------------------------------------- Time 69.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 15 llr = 291 E-value = 7.6e-034 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2a:11::3a::4a:2:3:8a: pos.-specific C 5:8:5a7::7:::23:57::: probability G 3:212::::3a6:65::3::a matrix T :::82:37:::::2:a2:2:: bits 2.2 * * 2.0 * * * * * ** 1.8 * * * * * * ** 1.6 * * * * * * ** Relative 1.3 ** * *** * * ** Entropy 1.1 ** ******** * **** (28.0 bits) 0.9 *** ******** * **** 0.7 **** *********** **** 0.4 **** **************** 0.2 ********************* 0.0 --------------------- Multilevel CACTCCCTACGGAGGTCCAAG consensus G G G TA G A CC AGT sequence A T TA T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36007 343 9.64e-12 TCCCCGAGGA CACTGCCTACGGAGGTAGAAG TGAGTGTACC 40611 330 9.64e-12 TCCCCGAGGA CACTGCCTACGGAGGTAGAAG TGAGTGTACC 38462 330 9.64e-12 TCCCCGAGGA CACTGCCTACGGAGGTAGAAG TGAGTGTACC 40968 343 3.59e-11 TCCCCGAGGA CACTACCTACGGAGGTAGAAG TGAGTGTACC 38903 343 3.59e-11 TCCACAAGGA CACTACCTACGGAGGTAGAAG TGAATGTACC 50643 202 7.62e-10 ATTCTACTGA GACTCCTAAGGGAGCTCCAAG GGATTTGTTT 49705 203 7.62e-10 ATTCTACTGA GACTCCTAAGGGAGCTCCAAG GGATTTGTTT 46978 221 7.62e-10 ATTCTACTGA GACTCCTAAGGGAGCTCCAAG GGATTTGTTT 31815 196 7.62e-10 ATTCTACTGA GACTCCTAAGGGAGCTCCAAG GGATTTGTTT 52461 324 8.43e-10 CACAGCCCCA CAGTCCCTACGAATATCCAAG AGTACAGTAT 39762 325 8.43e-10 CACAGCCCCA CAGTCCCTACGAATATCCAAG AGTACAGTAT 37580 325 8.43e-10 CACAGCCCCA CAGTCCCTACGAATATCCAAG AGCACATTGT 40608 161 1.05e-08 ACAGAGCTTT AACGTCCTACGAACGTTCTAG TCTTCCCGTT 38388 161 1.05e-08 ACAGAGCTTT AACGTCCTACGAACGTTCTAG TCTTCCCGTT 40843 161 1.46e-08 ACAGAGCTTT AACATCCTACGAACGTTCTAG TCTTCCCGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36007 9.6e-12 342_[+3]_137 40611 9.6e-12 329_[+3]_150 38462 9.6e-12 329_[+3]_150 40968 3.6e-11 342_[+3]_137 38903 3.6e-11 342_[+3]_137 50643 7.6e-10 201_[+3]_278 49705 7.6e-10 202_[+3]_277 46978 7.6e-10 220_[+3]_259 31815 7.6e-10 195_[+3]_284 52461 8.4e-10 323_[+3]_156 39762 8.4e-10 324_[+3]_155 37580 8.4e-10 324_[+3]_155 40608 1e-08 160_[+3]_319 38388 1e-08 160_[+3]_319 40843 1.5e-08 160_[+3]_319 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=15 36007 ( 343) CACTGCCTACGGAGGTAGAAG 1 40611 ( 330) CACTGCCTACGGAGGTAGAAG 1 38462 ( 330) CACTGCCTACGGAGGTAGAAG 1 40968 ( 343) CACTACCTACGGAGGTAGAAG 1 38903 ( 343) CACTACCTACGGAGGTAGAAG 1 50643 ( 202) GACTCCTAAGGGAGCTCCAAG 1 49705 ( 203) GACTCCTAAGGGAGCTCCAAG 1 46978 ( 221) GACTCCTAAGGGAGCTCCAAG 1 31815 ( 196) GACTCCTAAGGGAGCTCCAAG 1 52461 ( 324) CAGTCCCTACGAATATCCAAG 1 39762 ( 325) CAGTCCCTACGAATATCCAAG 1 37580 ( 325) CAGTCCCTACGAATATCCAAG 1 40608 ( 161) AACGTCCTACGAACGTTCTAG 1 38388 ( 161) AACGTCCTACGAACGTTCTAG 1 40843 ( 161) AACATCCTACGAACGTTCTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 32160 bayes= 11.7399 E= 7.6e-034 -42 117 31 -1055 190 -1055 -1055 -1055 -1055 176 -10 -1055 -200 -1055 -69 151 -100 98 -10 -49 -1055 208 -1055 -1055 -1055 163 -1055 -8 0 -1055 -1055 138 190 -1055 -1055 -1055 -1055 163 31 -1055 -1055 -1055 222 -1055 58 -1055 148 -1055 190 -1055 -1055 -1055 -1055 -24 148 -49 -42 17 131 -1055 -1055 -1055 -1055 183 32 98 -1055 -49 -1055 149 63 -1055 158 -1055 -1055 -49 190 -1055 -1055 -1055 -1055 -1055 222 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 15 E= 7.6e-034 0.200000 0.533333 0.266667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.066667 0.000000 0.133333 0.800000 0.133333 0.466667 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.733333 0.000000 0.266667 0.266667 0.000000 0.000000 0.733333 1.000000 0.000000 0.000000 0.000000 0.000000 0.733333 0.266667 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.200000 0.200000 0.266667 0.533333 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.466667 0.000000 0.200000 0.000000 0.666667 0.333333 0.000000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CGA]A[CG]T[CGT]C[CT][TA]A[CG]G[GA]A[GCT][GCA]T[CAT][CG][AT]AG -------------------------------------------------------------------------------- Time 102.15 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37297 2.17e-07 280_[+1(7.64e-08)]_143_\ [+2(5.58e-08)]_35 37580 1.96e-10 324_[+3(8.43e-10)]_50_\ [+2(4.96e-06)]_63_[+1(9.82e-07)] 37761 5.33e-01 500 38388 5.33e-11 160_[+3(1.05e-08)]_125_\ [+2(2.64e-07)]_79_[+1(3.66e-07)]_73 38409 4.95e-01 500 38462 8.92e-16 149_[+1(1.66e-08)]_159_\ [+3(9.64e-12)]_13_[+2(5.58e-08)]_116 48356 1.42e-02 170_[+1(1.46e-05)]_309 39076 8.45e-11 130_[+2(1.13e-08)]_33_\ [+1(9.14e-11)]_295 39129 5.92e-01 500 39223 8.45e-11 132_[+2(1.13e-08)]_33_\ [+1(9.14e-11)]_293 39341 4.32e-01 500 39762 1.62e-11 324_[+3(8.43e-10)]_50_\ [+2(9.84e-07)]_63_[+1(3.43e-07)] 39794 2.91e-01 500 40608 5.33e-11 160_[+3(1.05e-08)]_125_\ [+2(2.64e-07)]_79_[+1(3.66e-07)]_73 40611 4.13e-15 149_[+1(8.32e-08)]_159_\ [+3(9.64e-12)]_13_[+2(5.58e-08)]_116 40843 2.12e-11 160_[+3(1.46e-08)]_125_\ [+2(2.64e-07)]_79_[+1(9.82e-08)]_73 33124 2.23e-09 133_[+2(2.39e-07)]_33_\ [+1(1.36e-10)]_292 33729 2.10e-07 280_[+1(7.64e-08)]_143_\ [+2(5.58e-08)]_35 35442 2.14e-04 444_[+2(5.58e-08)]_35 36007 8.92e-16 4_[+2(4.50e-05)]_135_[+1(1.66e-08)]_\ 161_[+3(9.64e-12)]_13_[+2(5.58e-08)]_103 33184 3.38e-03 218_[+2(8.86e-06)]_20_\ [+2(7.17e-05)]_220 48336 3.06e-01 500 38903 1.33e-14 161_[+1(7.64e-08)]_160_\ [+3(3.59e-11)]_13_[+2(5.58e-08)]_103 10286 3.93e-01 500 31815 1.07e-15 14_[+2(1.65e-09)]_21_[+1(8.56e-09)]_\ 118_[+3(7.62e-10)]_284 39006 8.62e-01 500 33569 9.94e-01 500 48687 8.12e-01 500 33645 1.47e-07 128_[+2(1.67e-05)]_239_\ [+1(1.85e-08)]_33_[+2(5.76e-07)]_37 39222 1.44e-09 133_[+2(1.56e-07)]_33_\ [+1(1.36e-10)]_292 41458 6.09e-01 500 37057 1.95e-06 282_[+1(1.83e-07)]_141_\ [+2(3.57e-07)]_35 46978 2.39e-14 49_[+2(4.36e-08)]_11_[+1(8.56e-09)]_\ 118_[+3(7.62e-10)]_259 52461 8.57e-08 323_[+3(8.43e-10)]_51_\ [+2(4.96e-06)]_84 39391 5.15e-01 500 38408 7.24e-01 500 40228 4.76e-01 500 39509 7.01e-01 500 40645 3.08e-01 500 39668 4.50e-06 140_[+2(1.67e-05)]_230_\ [+1(2.12e-07)]_30_[+2(2.23e-06)]_37 46977 9.69e-11 173_[+2(1.13e-08)]_33_\ [+1(9.14e-11)]_252 37061 7.75e-01 500 40968 1.57e-13 5_[+2(4.50e-05)]_135_[+1(7.64e-08)]_\ 160_[+3(3.59e-11)]_13_[+2(7.56e-07)]_103 38262 1.99e-01 500 50211 6.90e-01 500 41117 5.38e-01 500 37400 9.95e-01 500 40570 2.02e-02 162_[+2(8.86e-06)]_317 37845 8.06e-01 500 48349 2.29e-01 213_[+1(5.11e-05)]_266 49959 9.76e-02 143_[+1(6.39e-05)]_336 37714 1.38e-01 20_[+1(8.14e-05)]_459 40525 9.25e-01 500 40625 1.45e-03 464_[+2(2.93e-07)]_15 41575 9.13e-07 281_[+1(7.64e-08)]_142_\ [+2(1.63e-06)]_35 39906 3.86e-01 500 38074 3.82e-01 500 35237 2.02e-02 162_[+2(8.86e-06)]_317 34587 1.45e-03 464_[+2(2.93e-07)]_15 49705 2.39e-14 11_[+2(4.36e-08)]_9_[+2(1.56e-07)]_\ 1_[+1(8.56e-09)]_118_[+3(7.62e-10)]_277 39360 7.04e-01 500 41578 9.27e-01 500 41582 4.88e-01 500 38156 6.09e-01 500 50643 2.39e-14 10_[+2(4.36e-08)]_9_[+2(1.56e-07)]_\ 1_[+1(8.56e-09)]_118_[+3(7.62e-10)]_278 54907 9.58e-01 500 39363 2.43e-06 120_[+2(1.67e-05)]_249_\ [+1(1.07e-07)]_31_[+2(2.23e-06)]_37 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************