******************************************************************************** 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/71/71.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10604 1.0000 500 11822 1.0000 500 1557 1.0000 500 1875 1.0000 500 21900 1.0000 500 22383 1.0000 500 24572 1.0000 500 256250 1.0000 500 261242 1.0000 500 263116 1.0000 500 263902 1.0000 500 31923 1.0000 500 3258 1.0000 500 33021 1.0000 500 33911 1.0000 500 36709 1.0000 500 37444 1.0000 500 37599 1.0000 500 38769 1.0000 500 3951 1.0000 500 4117 1.0000 500 6932 1.0000 500 7094 1.0000 500 7642 1.0000 500 8293 1.0000 500 9037 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/71/71.seqs.fa -oc motifs/71 -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= 26 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= 13000 N= 26 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.279 C 0.229 G 0.233 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.279 C 0.229 G 0.233 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 26 llr = 274 E-value = 1.9e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7:752752:287552634733 pos.-specific C :82582344613327355:74 probability G 2::::::131:::2::2:::: matrix T 121::123321:2211:13:3 bits 2.1 1.9 1.7 1.5 * * Relative 1.3 * * Entropy 1.1 * * ** ** (15.2 bits) 0.9 ****** ** * ** 0.6 ****** ** ****** 0.4 ******* **** ******* 0.2 ********************* 0.0 --------------------- Multilevel ACACCAACCCAAAACACCACC consensus A CTG CC ACAATAA sequence AT T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10604 464 9.31e-11 CACCATAAAT ACAACAACCCACAACACAACC TATCGACCCC 38769 402 4.16e-09 TCAGTCGCTG ACACCACCGCAAAACAACTCA CAAAGGATTG 11822 401 4.16e-09 TCAGTCGCTG ACACCACCGCAAAACAACTCA CAAAGGATTG 33021 52 3.51e-07 AAGCAAAGAA ACAACAATGGAAAGCAACAAC AAAGAGAGAG 256250 51 3.51e-07 AAGCAAAGAA ACAACAATGGAAAGCAACAAC AAAGAGAGAG 4117 434 5.79e-07 CATCACAGCG ACCACAACTCAACATCGCACC GCACTCAGCA 37599 336 6.54e-07 GCAATACAAT ACACAAAATCAATCCACATCC AACCATGCCC 37444 465 6.54e-07 AACAACCACC ACACCAAGCAAACAACACACC GATACAAGAG 7642 286 1.63e-06 CGACGTCGAC ACAACACTCTCACTCACCACT ACCAGCAGTA 263116 298 3.06e-06 CAGTGTCAGT GCACCTCGCCACCTCACCACT CTCCTCATCA 31923 38 3.39e-06 GATGAAAACA ACAACTATTCAACATTCAACT TCATGAATGA 1875 479 3.39e-06 GTCTGCGTCA ACAAAAACTCACAAACGAAAC C 263902 480 3.74e-06 TCCACTATCC TCAACACATCACCGACCAACT 22383 407 4.13e-06 TAATCAGTAT ACTACATAGGAAAACAGAACA GTGGATTAAA 8293 364 4.55e-06 CAGTGGACAA ATACCACGTCACTCCCCCAAC CTCTGAAGAC 33911 473 1.22e-05 CCCTTGACAA ACAACAAACCTCTCAACAAAT CAAACCA 36709 458 1.99e-05 CACCACACTC ATCCCTACTCAACACCGTACA CCTCCTTGAT 3258 266 2.15e-05 CTGACAAAGT GTCAAAACTCAAAACCAAACT TCCCGCAATC 3951 182 2.32e-05 TGTTCCATCA TCTCCATCGTAAAACTCCTCA TTGTTGGAAT 24572 480 2.50e-05 CAAATCACAC ACAGCAACCATCTGCACAACA 7094 476 2.69e-05 GGCTGAGTCA GTAACATCGCAAAGCACTTAA AAAA 21900 480 3.35e-05 ACGACCGACG GCACACAACCCCAACACCAAA 1557 460 3.85e-05 CACGCATCAC ACACCCCACTAAGTACCCTCC CTCCTCGGCT 261242 320 4.42e-05 GCTCTCTAGT ACTCCAGTCAAATCTACAACC GTGAGCATGT 9037 435 7.86e-05 TACCTTTTTA TCACCCCTCTAATTAAAAAAT CTAGAGAATA 6932 29 1.11e-04 GTCCTAATGG ACCCCCTTGAAAAACTGTTCT ATGTACTCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10604 9.3e-11 463_[+1]_16 38769 4.2e-09 401_[+1]_78 11822 4.2e-09 400_[+1]_79 33021 3.5e-07 51_[+1]_428 256250 3.5e-07 50_[+1]_429 4117 5.8e-07 433_[+1]_46 37599 6.5e-07 335_[+1]_144 37444 6.5e-07 464_[+1]_15 7642 1.6e-06 285_[+1]_194 263116 3.1e-06 297_[+1]_182 31923 3.4e-06 37_[+1]_442 1875 3.4e-06 478_[+1]_1 263902 3.7e-06 479_[+1] 22383 4.1e-06 406_[+1]_73 8293 4.5e-06 363_[+1]_116 33911 1.2e-05 472_[+1]_7 36709 2e-05 457_[+1]_22 3258 2.1e-05 265_[+1]_214 3951 2.3e-05 181_[+1]_298 24572 2.5e-05 479_[+1] 7094 2.7e-05 475_[+1]_4 21900 3.3e-05 479_[+1] 1557 3.9e-05 459_[+1]_20 261242 4.4e-05 319_[+1]_160 9037 7.9e-05 434_[+1]_45 6932 0.00011 28_[+1]_451 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=26 10604 ( 464) ACAACAACCCACAACACAACC 1 38769 ( 402) ACACCACCGCAAAACAACTCA 1 11822 ( 401) ACACCACCGCAAAACAACTCA 1 33021 ( 52) ACAACAATGGAAAGCAACAAC 1 256250 ( 51) ACAACAATGGAAAGCAACAAC 1 4117 ( 434) ACCACAACTCAACATCGCACC 1 37599 ( 336) ACACAAAATCAATCCACATCC 1 37444 ( 465) ACACCAAGCAAACAACACACC 1 7642 ( 286) ACAACACTCTCACTCACCACT 1 263116 ( 298) GCACCTCGCCACCTCACCACT 1 31923 ( 38) ACAACTATTCAACATTCAACT 1 1875 ( 479) ACAAAAACTCACAAACGAAAC 1 263902 ( 480) TCAACACATCACCGACCAACT 1 22383 ( 407) ACTACATAGGAAAACAGAACA 1 8293 ( 364) ATACCACGTCACTCCCCCAAC 1 33911 ( 473) ACAACAAACCTCTCAACAAAT 1 36709 ( 458) ATCCCTACTCAACACCGTACA 1 3258 ( 266) GTCAAAACTCAAAACCAAACT 1 3951 ( 182) TCTCCATCGTAAAACTCCTCA 1 24572 ( 480) ACAGCAACCATCTGCACAACA 1 7094 ( 476) GTAACATCGCAAAGCACTTAA 1 21900 ( 480) GCACACAACCCCAACACCAAA 1 1557 ( 460) ACACCCCACTAAGTACCCTCC 1 261242 ( 320) ACTCCAGTCAAATCTACAACC 1 9037 ( 435) TCACCCCTCTAATTAAAAAAT 1 6932 ( 29) ACCCCCTTGAAAAACTGTTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12480 bayes= 8.90388 E= 1.9e-006 139 -1134 -60 -117 -1134 189 -1134 -75 139 -57 -1134 -117 73 113 -260 -1134 -86 189 -1134 -1134 139 -57 -1134 -117 84 43 -260 -75 -27 75 -102 6 -1134 75 40 25 -86 133 -102 -75 160 -157 -1134 -175 131 43 -1134 -1134 73 23 -260 -17 84 -57 -28 -75 -27 151 -1134 -117 105 43 -1134 -117 -5 123 -28 -1134 60 101 -1134 -117 139 -1134 -1134 6 14 160 -1134 -1134 14 75 -1134 25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 1.9e-006 0.730769 0.000000 0.153846 0.115385 0.000000 0.846154 0.000000 0.153846 0.730769 0.153846 0.000000 0.115385 0.461538 0.500000 0.038462 0.000000 0.153846 0.846154 0.000000 0.000000 0.730769 0.153846 0.000000 0.115385 0.500000 0.307692 0.038462 0.153846 0.230769 0.384615 0.115385 0.269231 0.000000 0.384615 0.307692 0.307692 0.153846 0.576923 0.115385 0.153846 0.846154 0.076923 0.000000 0.076923 0.692308 0.307692 0.000000 0.000000 0.461538 0.269231 0.038462 0.230769 0.500000 0.153846 0.192308 0.153846 0.230769 0.653846 0.000000 0.115385 0.576923 0.307692 0.000000 0.115385 0.269231 0.538462 0.192308 0.000000 0.423077 0.461538 0.000000 0.115385 0.730769 0.000000 0.000000 0.269231 0.307692 0.692308 0.000000 0.000000 0.307692 0.384615 0.000000 0.307692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- ACA[CA]CA[AC][CTA][CGT]CA[AC][ACT]A[CA][AC][CA][CA][AT][CA][CAT] -------------------------------------------------------------------------------- Time 5.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 23 llr = 240 E-value = 2.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 24:2321131:3272: pos.-specific C :11:2:::::22211: probability G 6:9::8191:8161:9 matrix T 24:85:8:68:5:171 bits 2.1 1.9 1.7 * 1.5 * * * * Relative 1.3 ** * * * * Entropy 1.1 ** *** ** * (15.0 bits) 0.9 ** *** ** ** 0.6 * ** ****** **** 0.4 *********** **** 0.2 **************** 0.0 ---------------- Multilevel GAGTTGTGTTGTGATG consensus AT AA A AA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 38769 115 1.85e-09 GCAATTTGTT GAGTTGTGTTGAGATG TGTTGTGAGG 11822 114 1.85e-09 GCAATTTGTT GAGTTGTGTTGAGATG TGTTGTGAGG 21900 184 1.03e-07 AGCAGCTGCC ATCTTGTGTTGTGATG TAGGACGACG 33911 81 1.60e-07 AGGTGACGGT GCGTTGTGATGTGAAG GAGGTGACGG 37599 180 5.01e-07 TCCTCAACAC GTGATGTGATGTGACG TGACGAAAGA 37444 63 7.89e-07 GCATCCGATG GAGAAGTGATGGGATG GAATACACGT 22383 299 1.38e-06 ATGGTCTAGA GTGTAGTGTACCGATG GGTACCACCG 3951 449 4.22e-06 CAGCACAAAT GAGTTGAGTTGAAACG AGCAAGTGAA 10604 98 4.22e-06 AGTGTGGTTT GAGATATGTTGTAGTG AAACGAAGGA 33021 80 5.07e-06 AACAAAGAGA GAGTAGTAATGCCATG CATACAACCA 256250 79 5.07e-06 AACAAAGAGA GAGTAGTAATGCCATG CATACAACCA 263116 40 6.09e-06 GCTGGGTCCA TCGTTGGGTTGAAATG GTAGTTCAGG 7094 146 8.71e-06 GATTGCTTCG TTCTCGTGTTGTAGTG GCGCCATGAT 4117 256 1.22e-05 TGCGGCTTCG AAGTTGAGTTGTGAAT ACCATAGTAC 263902 221 1.22e-05 ATGATGAAGT TTGTTGTTTGGTGATG TATTGAAGGA 8293 109 1.33e-05 TCTTCTCATG ATGTAGTGTAGTGCAG AACGAGGTGA 3258 103 1.33e-05 TGCGCGATGG TTGTCGTGTTCGGCTG ATGATGGCTC 7642 323 1.83e-05 AGTAGCATTG GAGAAGAGAAGCGATG TAAAGAGCAG 9037 354 2.70e-05 TAGGGCAGCT GCGTTGTGGTTTGTTG GTGTAGCACT 24572 6 2.91e-05 GCTGT GACTTGGGTTGACTTG CAGTGTGGTA 1875 363 4.47e-05 TTGTATTTCA ATGTCATGTTCAGATT TTCGACCAAC 36709 127 5.13e-05 GCGAACCACG ATGACATGATGTAGTG ATTGTGTTTG 1557 266 8.64e-05 GATGTCTTCT TTGTAATGGTCTCAAG CAAGACGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38769 1.9e-09 114_[+2]_370 11822 1.9e-09 113_[+2]_371 21900 1e-07 183_[+2]_301 33911 1.6e-07 80_[+2]_404 37599 5e-07 179_[+2]_305 37444 7.9e-07 62_[+2]_422 22383 1.4e-06 298_[+2]_186 3951 4.2e-06 448_[+2]_36 10604 4.2e-06 97_[+2]_387 33021 5.1e-06 79_[+2]_405 256250 5.1e-06 78_[+2]_406 263116 6.1e-06 39_[+2]_445 7094 8.7e-06 145_[+2]_339 4117 1.2e-05 255_[+2]_229 263902 1.2e-05 220_[+2]_264 8293 1.3e-05 108_[+2]_376 3258 1.3e-05 102_[+2]_382 7642 1.8e-05 322_[+2]_162 9037 2.7e-05 353_[+2]_131 24572 2.9e-05 5_[+2]_479 1875 4.5e-05 362_[+2]_122 36709 5.1e-05 126_[+2]_358 1557 8.6e-05 265_[+2]_219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=23 38769 ( 115) GAGTTGTGTTGAGATG 1 11822 ( 114) GAGTTGTGTTGAGATG 1 21900 ( 184) ATCTTGTGTTGTGATG 1 33911 ( 81) GCGTTGTGATGTGAAG 1 37599 ( 180) GTGATGTGATGTGACG 1 37444 ( 63) GAGAAGTGATGGGATG 1 22383 ( 299) GTGTAGTGTACCGATG 1 3951 ( 449) GAGTTGAGTTGAAACG 1 10604 ( 98) GAGATATGTTGTAGTG 1 33021 ( 80) GAGTAGTAATGCCATG 1 256250 ( 79) GAGTAGTAATGCCATG 1 263116 ( 40) TCGTTGGGTTGAAATG 1 7094 ( 146) TTCTCGTGTTGTAGTG 1 4117 ( 256) AAGTTGAGTTGTGAAT 1 263902 ( 221) TTGTTGTTTGGTGATG 1 8293 ( 109) ATGTAGTGTAGTGCAG 1 3258 ( 103) TTGTCGTGTTCGGCTG 1 7642 ( 323) GAGAAGAGAAGCGATG 1 9037 ( 354) GCGTTGTGGTTTGTTG 1 24572 ( 6) GACTTGGGTTGACTTG 1 1875 ( 363) ATGTCATGTTCAGATT 1 36709 ( 127) ATGACATGATGTAGTG 1 1557 ( 266) TTGTAATGGTCTCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12610 bayes= 9.49927 E= 2.8e-006 -36 -1117 128 -25 64 -81 -1117 75 -1117 -81 190 -1117 -36 -1117 -1117 160 13 -40 -1117 101 -68 -1117 182 -1117 -109 -1117 -142 160 -168 -1117 190 -257 13 -1117 -142 123 -109 -1117 -242 167 -1117 -40 175 -257 -10 -40 -142 89 -36 -40 138 -1117 132 -140 -84 -157 -68 -140 -1117 151 -1117 -1117 197 -157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 2.8e-006 0.217391 0.000000 0.565217 0.217391 0.434783 0.130435 0.000000 0.434783 0.000000 0.130435 0.869565 0.000000 0.217391 0.000000 0.000000 0.782609 0.304348 0.173913 0.000000 0.521739 0.173913 0.000000 0.826087 0.000000 0.130435 0.000000 0.086957 0.782609 0.086957 0.000000 0.869565 0.043478 0.304348 0.000000 0.086957 0.608696 0.130435 0.000000 0.043478 0.826087 0.000000 0.173913 0.782609 0.043478 0.260870 0.173913 0.086957 0.478261 0.217391 0.173913 0.608696 0.000000 0.695652 0.086957 0.130435 0.086957 0.173913 0.086957 0.000000 0.739130 0.000000 0.000000 0.913043 0.086957 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GAT][AT]G[TA][TA]GTG[TA]TG[TA][GA]ATG -------------------------------------------------------------------------------- Time 10.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 20 llr = 215 E-value = 8.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1728:313113::19 pos.-specific C :2:::3:1:::2::1 probability G 92538:8:2a5189: matrix T 1:4:35278:3731: bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * * * *** Entropy 1.1 * ** * ** *** (15.5 bits) 0.9 * ** **** **** 0.6 ** ** **** **** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GAGAGTGTTGGTGGA consensus TGTA A ACT sequence A C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 7094 373 3.93e-08 AAGTGATGAG GAAAGTGTTGATGGA TGATCGAGGC 38769 72 2.74e-07 GAGCAGCGAT GATAGAGTTGTTTGA CATGGTATTG 11822 71 2.74e-07 GAGCAGCGAT GATAGAGTTGTTTGA CATGGTATTG 10604 72 3.11e-07 GATTTGGTTG GGGAGTGTGGGTGGA GAGTGTGGTT 33911 33 3.92e-07 GTGGCGAGTA GAGATTGTTGTTTGA GTTGGTGTAG 33021 231 1.70e-06 CATACACTCA GAGAGCGTTGACGGC ATCACGTGTC 256250 230 1.70e-06 CATACACTCA GAGAGCGTTGACGGC ATCACGTGTC 261242 174 2.54e-06 ATATCAAGTG GCAAGATTTGGTGGA TCCGACAGGT 1557 155 2.54e-06 CGAAGGAGGA GAAGGAATTGGTGGA GAAATTGCAA 3951 52 3.69e-06 CTGGATTGTT GGTGTTGTTGGTTGA CATCATATTT 263902 263 4.43e-06 GTCTCGAAAC GAAAGTTCTGGTGGA GAAGGGTGCA 3258 61 6.25e-06 CTTTCATAAT GATGGCGTTGATGAA GGATATCTTT 9037 126 8.76e-06 GACCCATGAT GCGATCGATGACGGA GGAGGCACCG 7642 32 1.11e-05 GTTGGCTGGG GAGAGTAAAGGTGGA TGATTAGGAG 4117 32 1.11e-05 TGGACAGCTA TCGAGTGTTGGGGGA GGACGAGTAA 37599 137 1.11e-05 ATCAAAAAAG GAGATCGAGGTCGGA GGCGGAGAGC 8293 314 1.50e-05 TAATGCATTC GATATTGTTAGGGGA CAAACAAGTT 21900 387 1.50e-05 ACAGGAGGTG AGGGGTGTTGGTTGA GCTTTGCGTC 1875 187 1.50e-05 AGAGAAAGTG GATAGAGAGGTTGTA GAAAGCGAGT 22383 186 3.24e-05 CATCGATCAG GATGGATATGATGTA CTCGGAGGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7094 3.9e-08 372_[+3]_113 38769 2.7e-07 71_[+3]_414 11822 2.7e-07 70_[+3]_415 10604 3.1e-07 71_[+3]_414 33911 3.9e-07 32_[+3]_453 33021 1.7e-06 230_[+3]_255 256250 1.7e-06 229_[+3]_256 261242 2.5e-06 173_[+3]_312 1557 2.5e-06 154_[+3]_331 3951 3.7e-06 51_[+3]_434 263902 4.4e-06 262_[+3]_223 3258 6.3e-06 60_[+3]_425 9037 8.8e-06 125_[+3]_360 7642 1.1e-05 31_[+3]_454 4117 1.1e-05 31_[+3]_454 37599 1.1e-05 136_[+3]_349 8293 1.5e-05 313_[+3]_172 21900 1.5e-05 386_[+3]_99 1875 1.5e-05 186_[+3]_299 22383 3.2e-05 185_[+3]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=20 7094 ( 373) GAAAGTGTTGATGGA 1 38769 ( 72) GATAGAGTTGTTTGA 1 11822 ( 71) GATAGAGTTGTTTGA 1 10604 ( 72) GGGAGTGTGGGTGGA 1 33911 ( 33) GAGATTGTTGTTTGA 1 33021 ( 231) GAGAGCGTTGACGGC 1 256250 ( 230) GAGAGCGTTGACGGC 1 261242 ( 174) GCAAGATTTGGTGGA 1 1557 ( 155) GAAGGAATTGGTGGA 1 3951 ( 52) GGTGTTGTTGGTTGA 1 263902 ( 263) GAAAGTTCTGGTGGA 1 3258 ( 61) GATGGCGTTGATGAA 1 9037 ( 126) GCGATCGATGACGGA 1 7642 ( 32) GAGAGTAAAGGTGGA 1 4117 ( 32) TCGAGTGTTGGGGGA 1 37599 ( 137) GAGATCGAGGTCGGA 1 8293 ( 314) GATATTGTTAGGGGA 1 21900 ( 387) AGGGGTGTTGGTTGA 1 1875 ( 187) GATAGAGAGGTTGTA 1 22383 ( 186) GATGGATATGATGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 12636 bayes= 9.55294 E= 8.0e-005 -248 -1097 195 -237 133 -61 -64 -1097 -48 -1097 95 43 143 -1097 10 -1097 -1097 -1097 168 -5 11 13 -1097 80 -148 -1097 168 -79 -16 -219 -1097 143 -248 -1097 -64 163 -248 -1097 202 -1097 11 -1097 95 -5 -1097 -19 -122 143 -1097 -1097 168 -5 -248 -1097 186 -137 169 -119 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 20 E= 8.0e-005 0.050000 0.000000 0.900000 0.050000 0.700000 0.150000 0.150000 0.000000 0.200000 0.000000 0.450000 0.350000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.300000 0.250000 0.000000 0.450000 0.100000 0.000000 0.750000 0.150000 0.250000 0.050000 0.000000 0.700000 0.050000 0.000000 0.150000 0.800000 0.050000 0.000000 0.950000 0.000000 0.300000 0.000000 0.450000 0.250000 0.000000 0.200000 0.100000 0.700000 0.000000 0.000000 0.750000 0.250000 0.050000 0.000000 0.850000 0.100000 0.900000 0.100000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GA[GTA][AG][GT][TAC]G[TA]TG[GAT][TC][GT]GA -------------------------------------------------------------------------------- Time 16.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10604 7.49e-12 71_[+3(3.11e-07)]_11_[+2(4.22e-06)]_\ 168_[+3(3.93e-05)]_167_[+1(9.31e-11)]_16 11822 1.63e-13 70_[+3(2.74e-07)]_28_[+2(1.85e-09)]_\ 271_[+1(4.16e-09)]_79 1557 1.03e-04 154_[+3(2.54e-06)]_96_\ [+2(8.64e-05)]_178_[+1(3.85e-05)]_20 1875 3.34e-05 186_[+3(1.50e-05)]_161_\ [+2(4.47e-05)]_100_[+1(3.39e-06)]_1 21900 1.16e-06 59_[+2(6.68e-06)]_108_\ [+2(1.03e-07)]_187_[+3(1.50e-05)]_78_[+1(3.35e-05)] 22383 3.62e-06 185_[+3(3.24e-05)]_98_\ [+2(1.38e-06)]_92_[+1(4.13e-06)]_73 24572 6.41e-03 5_[+2(2.91e-05)]_319_[+1(9.94e-05)]_\ 118_[+1(2.50e-05)] 256250 8.92e-08 50_[+1(3.51e-07)]_7_[+2(5.07e-06)]_\ 135_[+3(1.70e-06)]_256 261242 1.54e-03 173_[+3(2.54e-06)]_131_\ [+1(4.42e-05)]_160 263116 3.19e-04 39_[+2(6.09e-06)]_242_\ [+1(3.06e-06)]_182 263902 3.96e-06 220_[+2(1.22e-05)]_26_\ [+3(4.43e-06)]_202_[+1(3.74e-06)] 31923 2.13e-02 37_[+1(3.39e-06)]_442 3258 2.71e-05 60_[+3(6.25e-06)]_27_[+2(1.33e-05)]_\ 147_[+1(2.15e-05)]_214 33021 8.92e-08 51_[+1(3.51e-07)]_7_[+2(5.07e-06)]_\ 135_[+3(1.70e-06)]_255 33911 2.53e-08 32_[+3(3.92e-07)]_4_[+2(5.13e-05)]_\ 13_[+2(1.60e-07)]_176_[+3(9.91e-05)]_185_[+1(1.22e-05)]_7 36709 3.36e-03 126_[+2(5.13e-05)]_315_\ [+1(1.99e-05)]_22 37444 1.31e-05 62_[+2(7.89e-07)]_386_\ [+1(6.54e-07)]_15 37599 1.05e-07 136_[+3(1.11e-05)]_28_\ [+2(5.01e-07)]_140_[+1(6.54e-07)]_144 38769 1.63e-13 71_[+3(2.74e-07)]_28_[+2(1.85e-09)]_\ 271_[+1(4.16e-09)]_78 3951 6.60e-06 51_[+3(3.69e-06)]_115_\ [+1(2.32e-05)]_69_[+2(9.20e-05)]_161_[+2(4.22e-06)]_36 4117 1.69e-06 31_[+3(1.11e-05)]_209_\ [+2(1.22e-05)]_162_[+1(5.79e-07)]_46 6932 3.58e-01 500 7094 2.43e-07 145_[+2(8.71e-06)]_211_\ [+3(3.93e-08)]_88_[+1(2.69e-05)]_4 7642 6.12e-06 31_[+3(1.11e-05)]_239_\ [+1(1.63e-06)]_16_[+2(1.83e-05)]_162 8293 1.50e-05 108_[+2(1.33e-05)]_189_\ [+3(1.50e-05)]_35_[+1(4.55e-06)]_116 9037 2.04e-04 125_[+3(8.76e-06)]_213_\ [+2(2.70e-05)]_65_[+1(7.86e-05)]_45 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************