******************************************************************************** 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/416/416.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10945 1.0000 500 11213 1.0000 500 11341 1.0000 500 22670 1.0000 500 22671 1.0000 500 22721 1.0000 500 23040 1.0000 500 23160 1.0000 500 23716 1.0000 500 24379 1.0000 500 24448 1.0000 500 260922 1.0000 500 261158 1.0000 500 262236 1.0000 500 264005 1.0000 500 268280 1.0000 500 268374 1.0000 500 268581 1.0000 500 29861 1.0000 500 31818 1.0000 500 32366 1.0000 500 41979 1.0000 500 4355 1.0000 500 6048 1.0000 500 7134 1.0000 500 7491 1.0000 500 8778 1.0000 500 8909 1.0000 500 9499 1.0000 500 bd1849 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/416/416.seqs.fa -oc motifs/416 -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= 30 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= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.251 C 0.241 G 0.243 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.251 C 0.241 G 0.243 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 14 llr = 196 E-value = 1.5e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::111::2::::131:32: pos.-specific C 29577594913a915a149 probability G 3:3:::1:1:1::4:::11 matrix T 511115:4:96::14:631 bits 2.1 * * 1.8 * * 1.6 * * ** ** * 1.4 * * ** ** * Relative 1.2 * * ** ** * * Entropy 1.0 * ** ** ** * * (20.2 bits) 0.8 * **** ***** * * 0.6 * **** ***** *** * 0.4 ************* *** * 0.2 ******************* 0.0 ------------------- Multilevel TCCCCCCCCTTCCGCCTCC consensus G G T T C AT AT sequence C A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 41979 243 7.75e-10 CGCGCTCGAA TCCCCTCTCTTCCATCTTC CATGACGGAC 262236 435 2.20e-09 GTTCCACTTC TCCCCTCCCTCCCGCCAAC TCCCGAAGTC 11213 470 1.14e-08 CACCACGTCG TCTCCTCCCTCCCACCTTC ACTTGTGACA 29861 126 2.34e-08 GTTGTATCCT CCGACTCTCTTCCGTCTCC ATCACAAATT 268374 308 2.34e-08 GACACCTTCT GCCCCCCACTTCCATCCTC TACTCTTCAT 264005 264 3.28e-08 GCCCCCAAGC TCCCCTCCCTTCCGCCAAG CTTCCGTCCG 8778 468 1.83e-07 CAACGCACGC TCCAACCTCTCCCTCCTCC TCCAACGCCG 268280 471 3.79e-07 GACAGACCTG CCGCCTGCCTTCCGTCCAC TTTCCCTCCA 10945 180 5.11e-07 TGATACATTC GCTTTTCACTTCCACCTCC TTCCACCCCT 7134 398 5.49e-07 CGAATCGCCA TCACCCCTCTTCACTCTTC ATCACCATCA 24448 415 5.90e-07 GAAAAGACCT GCCCCCCCCCCCCCTCTGC TGCTGTCAAC 268581 251 9.54e-07 GCAAATGTCC TCGCACCAGTTCCTCCACC CGCCTTCCCA 11341 26 1.09e-06 GCGATGAACC GTCCTCCCCTTCCGCCTCT GCCAGAGCCT 22670 431 1.68e-06 AAAAGAAGTG CCGTCCCTCTGCCGACACC ACTCCAACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41979 7.8e-10 242_[+1]_239 262236 2.2e-09 434_[+1]_47 11213 1.1e-08 469_[+1]_12 29861 2.3e-08 125_[+1]_356 268374 2.3e-08 307_[+1]_174 264005 3.3e-08 263_[+1]_218 8778 1.8e-07 467_[+1]_14 268280 3.8e-07 470_[+1]_11 10945 5.1e-07 179_[+1]_302 7134 5.5e-07 397_[+1]_84 24448 5.9e-07 414_[+1]_67 268581 9.5e-07 250_[+1]_231 11341 1.1e-06 25_[+1]_456 22670 1.7e-06 430_[+1]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=14 41979 ( 243) TCCCCTCTCTTCCATCTTC 1 262236 ( 435) TCCCCTCCCTCCCGCCAAC 1 11213 ( 470) TCTCCTCCCTCCCACCTTC 1 29861 ( 126) CCGACTCTCTTCCGTCTCC 1 268374 ( 308) GCCCCCCACTTCCATCCTC 1 264005 ( 264) TCCCCTCCCTTCCGCCAAG 1 8778 ( 468) TCCAACCTCTCCCTCCTCC 1 268280 ( 471) CCGCCTGCCTTCCGTCCAC 1 10945 ( 180) GCTTTTCACTTCCACCTCC 1 7134 ( 398) TCACCCCTCTTCACTCTTC 1 24448 ( 415) GCCCCCCCCCCCCCTCTGC 1 268581 ( 251) TCGCACCAGTTCCTCCACC 1 11341 ( 26) GTCCTCCCCTTCCGCCTCT 1 22670 ( 431) CCGTCCCTCTGCCGACACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 14460 bayes= 11.2342 E= 1.5e-007 -1045 -17 23 92 -1045 195 -1045 -189 -181 105 23 -89 -81 157 -1045 -89 -81 157 -1045 -89 -1045 105 -1045 92 -1045 195 -177 -1045 -23 83 -1045 43 -1045 195 -177 -1045 -1045 -175 -1045 181 -1045 25 -177 128 -1045 205 -1045 -1045 -181 195 -1045 -1045 18 -75 82 -89 -181 105 -1045 69 -1045 205 -1045 -1045 18 -75 -1045 111 -23 83 -177 11 -1045 183 -177 -189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 14 E= 1.5e-007 0.000000 0.214286 0.285714 0.500000 0.000000 0.928571 0.000000 0.071429 0.071429 0.500000 0.285714 0.142857 0.142857 0.714286 0.000000 0.142857 0.142857 0.714286 0.000000 0.142857 0.000000 0.500000 0.000000 0.500000 0.000000 0.928571 0.071429 0.000000 0.214286 0.428571 0.000000 0.357143 0.000000 0.928571 0.071429 0.000000 0.000000 0.071429 0.000000 0.928571 0.000000 0.285714 0.071429 0.642857 0.000000 1.000000 0.000000 0.000000 0.071429 0.928571 0.000000 0.000000 0.285714 0.142857 0.428571 0.142857 0.071429 0.500000 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.285714 0.142857 0.000000 0.571429 0.214286 0.428571 0.071429 0.285714 0.000000 0.857143 0.071429 0.071429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TGC]C[CG]CC[CT]C[CTA]CT[TC]CC[GA][CT]C[TA][CTA]C -------------------------------------------------------------------------------- Time 7.61 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 23 llr = 272 E-value = 3.5e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 44:24::32:3::2516131: pos.-specific C :::2:211:::::::::12:: probability G 61363:82:831871738247 matrix T :57:3814825821321:353 bits 2.1 1.8 1.6 1.4 * * Relative 1.2 * ** * Entropy 1.0 * ** ** ** * * * (17.0 bits) 0.8 * * ** ** *** * * * 0.6 **** ** ** ******* ** 0.4 ******* ********** ** 0.2 ****************** ** 0.0 --------------------- Multilevel GTTGATGTTGTTGGAGAGTTG consensus AAGAG AA A AT G AGT sequence CT G G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7491 4 2.24e-12 CGA GTTGGTGTTGTTGGAGAGTGG CGCCAGGGGA 32366 362 7.74e-09 GAGGAGGGAG GATGATGGTGGTGGGGAGGGG AATATGATGT 268280 163 1.65e-08 GTTTGGTGAA ATGGATGTTGTTGGATGGTGG CGTTGGTTGT 22671 7 2.95e-08 AGTGAC GTTGGTGTAGATTGTGAGTTG TAGTAATCAA 8909 160 8.31e-08 GGGGACATTG ATGGGTGTTGATGGATGGCTG GCACGACATG 264005 42 1.07e-07 AGGGCTACAG GTTCGTGTAGTTGGAGGAAGG GGATCTCCTT 24379 476 1.70e-07 TGAGGAGGGA AATAATGATGGTGGAAAGGGG GGAG 22721 72 2.40e-07 GAAGAAGGAG GATGTCTTTGATGGAGAGTTT GCAATGAACG 23716 357 2.68e-07 CGGCGTCGGT GGTGGTGGTGTTTGAGAGGAG ACTCTTTCGC 7134 282 1.91e-06 GAGTGAGTAC GATAGTGATGATGATGTAATG GAGTTATATT 4355 14 2.27e-06 ATTTGCAATT GACGACGGTGGTGGAGTGCGG GAGTGTGATG 22670 256 2.47e-06 AGAATCGGCC ATGCTCGTTGTTTGTGAGTGT AAAATGTGGT 261158 410 2.69e-06 AACTAGCCAC GTTCTTGAAGATGGTAAGAAG AATACACCAT 24448 236 4.05e-06 CTCCTGATTT AATGATGCAGAGGGTGAGCTT GTGTTGGTCT 6048 126 5.53e-06 GCAATACGTT GGTCTTCTTGTTGGTGAGTTC AGTTTTTGTT 11213 36 5.97e-06 GTGGTTGACG GATGGTGTTTTTGTGTTGATG GATGGAGTGA 262236 61 7.46e-06 GTGCTCTGCT GTGGTTGTTGGTTATTACTTG CATTGTCGGA 11341 298 7.46e-06 GCCTGCTTGG GATGGTGCTTTGGGTGGCATG TTGACTTGAT 31818 289 8.02e-06 GCCATCTATC AAGAATGGTTTAGAAGAGATG CTGGTAGAAC 268581 187 8.02e-06 AACAATAGCA AATAATGATGTCGAGGAGGTT GATGAAACCC 8778 248 8.62e-06 TTGGATCCGG ATGAACTATGGTGAAGGGCGG ATCAAAGCAG 268374 57 1.31e-05 TGCTTGCCAT GTTGTTTGTTTTGTAGGGTAT CTGAAAATAT 23160 132 1.40e-05 GTGTCGGTGT ATTCATCAAGGTGGAGGAGGT TGCAACTGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7491 2.2e-12 3_[+2]_476 32366 7.7e-09 361_[+2]_118 268280 1.7e-08 162_[+2]_317 22671 2.9e-08 6_[+2]_473 8909 8.3e-08 159_[+2]_320 264005 1.1e-07 41_[+2]_438 24379 1.7e-07 475_[+2]_4 22721 2.4e-07 71_[+2]_408 23716 2.7e-07 356_[+2]_123 7134 1.9e-06 281_[+2]_198 4355 2.3e-06 13_[+2]_466 22670 2.5e-06 255_[+2]_224 261158 2.7e-06 409_[+2]_70 24448 4.1e-06 235_[+2]_244 6048 5.5e-06 125_[+2]_354 11213 6e-06 35_[+2]_444 262236 7.5e-06 60_[+2]_419 11341 7.5e-06 297_[+2]_182 31818 8e-06 288_[+2]_191 268581 8e-06 186_[+2]_293 8778 8.6e-06 247_[+2]_232 268374 1.3e-05 56_[+2]_423 23160 1.4e-05 131_[+2]_348 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=23 7491 ( 4) GTTGGTGTTGTTGGAGAGTGG 1 32366 ( 362) GATGATGGTGGTGGGGAGGGG 1 268280 ( 163) ATGGATGTTGTTGGATGGTGG 1 22671 ( 7) GTTGGTGTAGATTGTGAGTTG 1 8909 ( 160) ATGGGTGTTGATGGATGGCTG 1 264005 ( 42) GTTCGTGTAGTTGGAGGAAGG 1 24379 ( 476) AATAATGATGGTGGAAAGGGG 1 22721 ( 72) GATGTCTTTGATGGAGAGTTT 1 23716 ( 357) GGTGGTGGTGTTTGAGAGGAG 1 7134 ( 282) GATAGTGATGATGATGTAATG 1 4355 ( 14) GACGACGGTGGTGGAGTGCGG 1 22670 ( 256) ATGCTCGTTGTTTGTGAGTGT 1 261158 ( 410) GTTCTTGAAGATGGTAAGAAG 1 24448 ( 236) AATGATGCAGAGGGTGAGCTT 1 6048 ( 126) GGTCTTCTTGTTGGTGAGTTC 1 11213 ( 36) GATGGTGTTTTTGTGTTGATG 1 262236 ( 61) GTGGTTGTTGGTTATTACTTG 1 11341 ( 298) GATGGTGCTTTGGGTGGCATG 1 31818 ( 289) AAGAATGGTTTAGAAGAGATG 1 268581 ( 187) AATAATGATGTCGAGGAGGTT 1 8778 ( 248) ATGAACTATGGTGAAGGGCGG 1 268374 ( 57) GTTGTTTGTTTTGTAGGGTAT 1 23160 ( 132) ATTCATCAAGGTGGAGGAGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 9.69102 E= 3.5e-007 64 -1117 132 -1117 79 -1117 -148 85 -1117 -247 10 139 -21 -15 122 -1117 64 -1117 52 -2 -1117 -47 -1117 164 -1117 -147 168 -102 5 -147 -16 72 -21 -1117 -1117 156 -1117 -1117 176 -61 5 -1117 10 85 -253 -247 -148 164 -1117 -1117 176 -61 -21 -1117 152 -160 105 -1117 -90 39 -153 -1117 160 -61 117 -1117 32 -102 -95 -147 168 -1117 5 -47 -16 39 -95 -1117 69 85 -1117 -247 152 -2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 23 E= 3.5e-007 0.391304 0.000000 0.608696 0.000000 0.434783 0.000000 0.086957 0.478261 0.000000 0.043478 0.260870 0.695652 0.217391 0.217391 0.565217 0.000000 0.391304 0.000000 0.347826 0.260870 0.000000 0.173913 0.000000 0.826087 0.000000 0.086957 0.782609 0.130435 0.260870 0.086957 0.217391 0.434783 0.217391 0.000000 0.000000 0.782609 0.000000 0.000000 0.826087 0.173913 0.260870 0.000000 0.260870 0.478261 0.043478 0.043478 0.086957 0.826087 0.000000 0.000000 0.826087 0.173913 0.217391 0.000000 0.695652 0.086957 0.521739 0.000000 0.130435 0.347826 0.086957 0.000000 0.739130 0.173913 0.565217 0.000000 0.304348 0.130435 0.130435 0.086957 0.782609 0.000000 0.260870 0.173913 0.217391 0.347826 0.130435 0.000000 0.391304 0.478261 0.000000 0.043478 0.695652 0.260870 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][TA][TG][GAC][AGT]TG[TAG][TA]G[TAG]TG[GA][AT]G[AG]G[TAG][TG][GT] -------------------------------------------------------------------------------- Time 14.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 20 llr = 228 E-value = 7.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 492:75:52461187183:6 pos.-specific C 1:411::24:2:311::::2 probability G 5:2a23a34512712a1363 matrix T 113:13:12228::2:144: bits 2.1 * 1.8 * * * 1.6 * * * 1.4 * * * * Relative 1.2 * * * * Entropy 1.0 * * * * ** * (16.5 bits) 0.8 * * * *** ** * 0.6 * ** * * ****** ** 0.4 * **** *********** 0.2 ** ***************** 0.0 -------------------- Multilevel GACGAAGACGATGAAGATGA consensus A T G GGA C ATG sequence A T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 22721 397 1.38e-08 CATTGAGGCA CACGAGGCGGATGAAGATGA AACTACAGAA 268374 3 2.54e-08 GT GATGAAGACGAGGAGGAGGA ACCACACTAT 262236 283 2.94e-08 TTGTCGCAGC AAAGAAGACAAGCAAGAGGA GTAGCGGCTG 24379 56 2.94e-08 GGCAGAAATA AAGGAGGACGATGATGATTA CAGCAACCAC 41979 4 5.18e-08 GAA GAAGAAGGGGAAGAAGAGTA CGAGTGATGA 24448 80 4.18e-07 TCCACGTGCT CATGAAGGGACTGAAGAATG AAGCACAAAA 23040 24 7.14e-07 TTCGATTGAA GACGAAGTTAATCAAGGAGA AGGTGTATTG 4355 151 8.77e-07 TGTTGCAACT GACGAGGACGGTGGTGAGGA CTGTGATAGC 6048 249 2.29e-06 TATTCTATTG GAAGAGGAGATTCCAGAAGC AATCCAATTA 11341 199 2.74e-06 ACGATCAGAT GATGATGTGTTTGCAGATGA TGCAGCACCG 32366 137 2.99e-06 GGAGAGTGGC GACGATGGTGATGATAATTA CGGTGGTAGC 261158 45 2.99e-06 CAACGGGAGC ATTGAAGAGTATGGAGATTG CAAAGCCATC bd1849 241 3.88e-06 TTTCAACAAT AATGAAGACAGAGAGGAATG AGACAAGGAG 9499 269 4.59e-06 GCATCCATTT GACGTTGGTATTCAAGAAGG TACAGGTGTC 11213 204 6.87e-06 GTGGTCGGTG ATCGGTGCCGATGAAGGGGA GGTGTTTACT 31818 128 8.02e-06 CAAGTCTGAG GAAGGTGCAACTGAAGAGTC AATTGAGGAG 7491 247 1.01e-05 CTTCACCACC AACGGAGAGGAGAACGATGA CACGACAGGA 268280 55 1.45e-05 TGCGTCTGTG TAGGCGGAAGATGAGGATGC AACGGTGGCA 264005 195 1.78e-05 TAATCATATT TAGGTGGACAATCAAGTATG GAGGAAAGGC 22670 387 3.39e-05 GCAGTGTGAA AATCAAGGATCTCAAGTTGA ATAGATTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22721 1.4e-08 396_[+3]_84 268374 2.5e-08 2_[+3]_478 262236 2.9e-08 282_[+3]_198 24379 2.9e-08 55_[+3]_425 41979 5.2e-08 3_[+3]_477 24448 4.2e-07 79_[+3]_401 23040 7.1e-07 23_[+3]_457 4355 8.8e-07 150_[+3]_330 6048 2.3e-06 248_[+3]_232 11341 2.7e-06 198_[+3]_282 32366 3e-06 136_[+3]_344 261158 3e-06 44_[+3]_436 bd1849 3.9e-06 240_[+3]_240 9499 4.6e-06 268_[+3]_212 11213 6.9e-06 203_[+3]_277 31818 8e-06 127_[+3]_353 7491 1e-05 246_[+3]_234 268280 1.4e-05 54_[+3]_426 264005 1.8e-05 194_[+3]_286 22670 3.4e-05 386_[+3]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=20 22721 ( 397) CACGAGGCGGATGAAGATGA 1 268374 ( 3) GATGAAGACGAGGAGGAGGA 1 262236 ( 283) AAAGAAGACAAGCAAGAGGA 1 24379 ( 56) AAGGAGGACGATGATGATTA 1 41979 ( 4) GAAGAAGGGGAAGAAGAGTA 1 24448 ( 80) CATGAAGGGACTGAAGAATG 1 23040 ( 24) GACGAAGTTAATCAAGGAGA 1 4355 ( 151) GACGAGGACGGTGGTGAGGA 1 6048 ( 249) GAAGAGGAGATTCCAGAAGC 1 11341 ( 199) GATGATGTGTTTGCAGATGA 1 32366 ( 137) GACGATGGTGATGATAATTA 1 261158 ( 45) ATTGAAGAGTATGGAGATTG 1 bd1849 ( 241) AATGAAGACAGAGAGGAATG 1 9499 ( 269) GACGTTGGTATTCAAGAAGG 1 11213 ( 204) ATCGGTGCCGATGAAGGGGA 1 31818 ( 128) GAAGGTGCAACTGAAGAGTC 1 7491 ( 247) AACGGAGAGGAGAACGATGA 1 268280 ( 55) TAGGCGGAAGATGAGGATGC 1 264005 ( 195) TAGGTGGACAATCAAGTATG 1 22670 ( 387) AATCAAGGATCTCAAGTTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14430 bayes= 9.74471 E= 7.0e-001 48 -127 89 -140 184 -1097 -1097 -140 -33 54 -70 18 -1097 -226 196 -1097 148 -226 -70 -140 84 -1097 30 -8 -1097 -1097 204 -1097 99 -68 4 -140 -74 54 52 -82 67 -1097 89 -82 125 -68 -128 -82 -133 -1097 -70 150 -233 32 142 -1097 167 -127 -128 -1097 137 -226 -70 -82 -233 -1097 196 -1097 167 -1097 -128 -140 25 -1097 30 60 -1097 -1097 130 60 125 -68 4 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 20 E= 7.0e-001 0.350000 0.100000 0.450000 0.100000 0.900000 0.000000 0.000000 0.100000 0.200000 0.350000 0.150000 0.300000 0.000000 0.050000 0.950000 0.000000 0.700000 0.050000 0.150000 0.100000 0.450000 0.000000 0.300000 0.250000 0.000000 0.000000 1.000000 0.000000 0.500000 0.150000 0.250000 0.100000 0.150000 0.350000 0.350000 0.150000 0.400000 0.000000 0.450000 0.150000 0.600000 0.150000 0.100000 0.150000 0.100000 0.000000 0.150000 0.750000 0.050000 0.300000 0.650000 0.000000 0.800000 0.100000 0.100000 0.000000 0.650000 0.050000 0.150000 0.150000 0.050000 0.000000 0.950000 0.000000 0.800000 0.000000 0.100000 0.100000 0.300000 0.000000 0.300000 0.400000 0.000000 0.000000 0.600000 0.400000 0.600000 0.150000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA]A[CTA]GA[AGT]G[AG][CG][GA]AT[GC]AAGA[TAG][GT][AG] -------------------------------------------------------------------------------- Time 21.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10945 1.66e-03 179_[+1(5.11e-07)]_302 11213 1.59e-08 35_[+2(5.97e-06)]_147_\ [+3(6.87e-06)]_246_[+1(1.14e-08)]_12 11341 5.36e-07 25_[+1(1.09e-06)]_154_\ [+3(2.74e-06)]_79_[+2(7.46e-06)]_182 22670 2.80e-06 191_[+2(1.40e-05)]_43_\ [+2(2.47e-06)]_110_[+3(3.39e-05)]_24_[+1(1.68e-06)]_51 22671 2.85e-04 6_[+2(2.95e-08)]_473 22721 1.69e-07 71_[+2(2.40e-07)]_304_\ [+3(1.38e-08)]_84 23040 2.29e-03 23_[+3(7.14e-07)]_457 23160 3.18e-02 131_[+2(1.40e-05)]_348 23716 2.68e-04 20_[+2(1.70e-05)]_315_\ [+2(2.68e-07)]_24_[+2(6.86e-05)]_78 24379 1.29e-07 55_[+3(2.94e-08)]_7_[+3(4.30e-05)]_\ 373_[+2(1.70e-07)]_4 24448 3.19e-08 79_[+3(4.18e-07)]_136_\ [+2(4.05e-06)]_158_[+1(5.90e-07)]_67 260922 4.47e-02 500 261158 1.18e-04 44_[+3(2.99e-06)]_345_\ [+2(2.69e-06)]_70 262236 2.68e-11 60_[+2(7.46e-06)]_201_\ [+3(2.94e-08)]_132_[+1(2.20e-09)]_8_[+1(9.84e-05)]_20 264005 2.46e-09 3_[+2(9.49e-05)]_17_[+2(1.07e-07)]_\ 132_[+3(1.78e-05)]_49_[+1(3.28e-08)]_218 268280 3.48e-09 54_[+3(1.45e-05)]_88_[+2(1.65e-08)]_\ 287_[+1(3.79e-07)]_11 268374 3.57e-10 2_[+3(2.54e-08)]_34_[+2(1.31e-05)]_\ 230_[+1(2.34e-08)]_174 268581 9.38e-07 189_[+3(5.40e-06)]_41_\ [+1(9.54e-07)]_231 29861 6.77e-04 125_[+1(2.34e-08)]_213_\ [+1(2.05e-05)]_124 31818 1.05e-03 127_[+3(8.02e-06)]_141_\ [+2(8.02e-06)]_191 32366 1.07e-06 4_[+2(2.77e-05)]_89_[+2(9.07e-05)]_\ 1_[+3(2.99e-06)]_64_[+2(3.90e-05)]_120_[+2(7.74e-09)]_118 41979 2.27e-09 3_[+3(5.18e-08)]_219_[+1(7.75e-10)]_\ 20_[+1(4.75e-07)]_200 4355 8.29e-06 13_[+2(2.27e-06)]_116_\ [+3(8.77e-07)]_330 6048 2.37e-04 125_[+2(5.53e-06)]_102_\ [+3(2.29e-06)]_232 7134 2.00e-05 1_[+1(1.08e-05)]_261_[+2(1.91e-06)]_\ 95_[+1(5.49e-07)]_84 7491 1.75e-09 3_[+2(2.24e-12)]_8_[+3(5.41e-05)]_\ 194_[+3(1.01e-05)]_96_[+3(8.28e-05)]_118 8778 4.19e-05 247_[+2(8.62e-06)]_199_\ [+1(1.83e-07)]_14 8909 1.19e-05 159_[+2(8.31e-08)]_320 9499 1.33e-02 268_[+3(4.59e-06)]_212 bd1849 2.88e-02 240_[+3(3.88e-06)]_240 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************