******************************************************************************** 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/23/23.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 12234 1.0000 500 1965 1.0000 500 21081 1.0000 500 21821 1.0000 500 22396 1.0000 500 22768 1.0000 500 24082 1.0000 500 24399 1.0000 500 25839 1.0000 500 260953 1.0000 500 260974 1.0000 500 261748 1.0000 500 262796 1.0000 500 262849 1.0000 500 268908 1.0000 500 270301 1.0000 500 270376 1.0000 500 28326 1.0000 500 28521 1.0000 500 30747 1.0000 500 31673 1.0000 500 32955 1.0000 500 33000 1.0000 500 3353 1.0000 500 33663 1.0000 500 34585 1.0000 500 36208 1.0000 500 36462 1.0000 500 6770 1.0000 500 9352 1.0000 500 9485 1.0000 500 bd846 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/23/23.seqs.fa -oc motifs/23 -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= 32 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= 16000 N= 32 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.274 C 0.237 G 0.230 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.237 G 0.230 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 32 llr = 302 E-value = 3.9e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 18332:8734328317 pos.-specific C 7:663a:283481491 probability G ::::2:21:31::1:: matrix T 22::3::::12112:2 bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * * * * (13.6 bits) 0.8 *** **** ** ** 0.6 **** **** ** ** 0.4 **** **** ** ** 0.2 **** *********** 0.0 ---------------- Multilevel CACCCCAACACCACCA consensus AAT CACA A sequence G GT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 36462 37 2.99e-09 CCTTCCTCGC CAACCCAACACCACCA CACCCAAACC bd846 107 1.53e-07 CACGATATGC CACCTCAAACCCAACA CCGTAATTCA 9485 386 1.82e-07 AAAACAACAA CAACCCAACACAACCA CCTGCATAAC 28326 246 2.15e-07 TTGATCGCCA CAAACCACCGCCACCA TGAAGTTCAC 270376 485 2.15e-07 TTGATCGCCA CAAACCACCGCCACCA 33663 440 2.50e-07 CGTCTCACAA CACCGCGACCACACCA CCCTCCACCT 270301 420 2.50e-07 CGTCTCACAA CACCGCGACCACACCA CCCTCCACCT 22768 108 6.12e-07 CTCTACCAGA CACAACAACATCATCA TTGCATCATC 24082 223 1.55e-06 CGACCGCCAG TAACCCAACAACAGCA CCGACCGGTT 1965 315 1.55e-06 CAAATCCAAC CACATCGACATCAACA ACTACGACAA 262849 483 3.17e-06 CATCACCATA CACCCCAACAGAAACA CC 32955 128 4.43e-06 TGCGACAGAG CACCGCGAAACCCCCA TAATCCACCG 25839 418 4.95e-06 TGTAGTTGTC TTCCACACCACCACCA TAGCTCCTCT 21081 464 5.53e-06 TCTTCTATCT CTCCTCAAACCCTCCA GTACACCATA 260974 474 1.25e-05 TTCCAACCGT TACAACACCGACATCA TTTGCTACAC 6770 34 1.37e-05 TGATGGGTGT CACATCAAATCCTCCA ACATTCACAC 30747 11 1.37e-05 AAAAGCATAC CACCTCTACACCAGCT ACTTTGACCG 260953 260 1.99e-05 CTTGTCCTAA CAAAGCAGAGCCATCA GATCATTTGC 28521 130 2.18e-05 GCACATAAGT CTCCTCACCAACACAA CTTCGAATAT 12234 469 2.18e-05 GCTGTCGGTG CACCTTAACACAAACA GCTCCATACT 36208 313 3.96e-05 TAACTAACGA CAACCCAACCTCCAAA GCAAAGCAGC 24399 466 3.96e-05 CCACCACTCA ATACACAACGTCAACA ACATAAATAC 21821 441 4.66e-05 GGTGGACTGA CACCCCCACGTCAGCC CACTTAAATC 3353 478 5.05e-05 CCATCTCTAC CACCACAACCAACACT ATCAACC 34585 182 5.46e-05 CGATCCTGCG AACACCACAGCCATCT TCTTCTCTCT 268908 35 7.42e-05 CGTCTGCATT CACATCACCGTTATCT ATCAAGACAC 262796 10 8.61e-05 ACATCGTTC ATCCGCAACCACTCCT AACAATGTAC 33000 105 1.83e-04 ACGTTAGAAG TATCTCAAACGCATCA GGATCTTGAT 261748 92 1.83e-04 CTAATTGATG CAAGCCAAAGTCAGCC AGCGTGGCAG 31673 459 1.95e-04 AGCTGGAGAA TACAGCGACTATACCA CACCACTTCA 22396 165 3.00e-04 CAAAGTCGTC CTATCCAACCCCCTCC CCCGATTATA 9352 309 8.59e-04 CCGACTTTGA TAAAGCAGCAAATACT TCATTGTGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36462 3e-09 36_[+1]_448 bd846 1.5e-07 106_[+1]_378 9485 1.8e-07 385_[+1]_99 28326 2.2e-07 245_[+1]_239 270376 2.2e-07 484_[+1] 33663 2.5e-07 439_[+1]_45 270301 2.5e-07 419_[+1]_65 22768 6.1e-07 107_[+1]_377 24082 1.5e-06 222_[+1]_262 1965 1.5e-06 314_[+1]_170 262849 3.2e-06 482_[+1]_2 32955 4.4e-06 127_[+1]_357 25839 4.9e-06 417_[+1]_67 21081 5.5e-06 463_[+1]_21 260974 1.2e-05 473_[+1]_11 6770 1.4e-05 33_[+1]_451 30747 1.4e-05 10_[+1]_474 260953 2e-05 259_[+1]_225 28521 2.2e-05 129_[+1]_355 12234 2.2e-05 468_[+1]_16 36208 4e-05 312_[+1]_172 24399 4e-05 465_[+1]_19 21821 4.7e-05 440_[+1]_44 3353 5e-05 477_[+1]_7 34585 5.5e-05 181_[+1]_303 268908 7.4e-05 34_[+1]_450 262796 8.6e-05 9_[+1]_475 33000 0.00018 104_[+1]_380 261748 0.00018 91_[+1]_393 31673 0.0002 458_[+1]_26 22396 0.0003 164_[+1]_320 9352 0.00086 308_[+1]_176 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=32 36462 ( 37) CAACCCAACACCACCA 1 bd846 ( 107) CACCTCAAACCCAACA 1 9485 ( 386) CAACCCAACACAACCA 1 28326 ( 246) CAAACCACCGCCACCA 1 270376 ( 485) CAAACCACCGCCACCA 1 33663 ( 440) CACCGCGACCACACCA 1 270301 ( 420) CACCGCGACCACACCA 1 22768 ( 108) CACAACAACATCATCA 1 24082 ( 223) TAACCCAACAACAGCA 1 1965 ( 315) CACATCGACATCAACA 1 262849 ( 483) CACCCCAACAGAAACA 1 32955 ( 128) CACCGCGAAACCCCCA 1 25839 ( 418) TTCCACACCACCACCA 1 21081 ( 464) CTCCTCAAACCCTCCA 1 260974 ( 474) TACAACACCGACATCA 1 6770 ( 34) CACATCAAATCCTCCA 1 30747 ( 11) CACCTCTACACCAGCT 1 260953 ( 260) CAAAGCAGAGCCATCA 1 28521 ( 130) CTCCTCACCAACACAA 1 12234 ( 469) CACCTTAACACAAACA 1 36208 ( 313) CAACCCAACCTCCAAA 1 24399 ( 466) ATACACAACGTCAACA 1 21821 ( 441) CACCCCCACGTCAGCC 1 3353 ( 478) CACCACAACCAACACT 1 34585 ( 182) AACACCACAGCCATCT 1 268908 ( 35) CACATCACCGTTATCT 1 262796 ( 10) ATCCGCAACCACTCCT 1 33000 ( 105) TATCTCAAACGCATCA 1 261748 ( 92) CAAGCCAAAGTCAGCC 1 31673 ( 459) TACAGCGACTATACCA 1 22396 ( 165) CTATCCAACCCCCTCC 1 9352 ( 309) TAAAGCAGCAAATACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 8.91886 E= 3.9e-011 -154 160 -1164 -47 157 -1164 -1164 -47 33 140 -1164 -305 33 132 -288 -305 -81 54 -7 12 -1164 203 -1164 -305 151 -292 -56 -305 139 -12 -188 -1164 -13 166 -1164 -1164 46 25 29 -205 4 88 -188 -24 -81 172 -1164 -205 146 -92 -1164 -105 -13 78 -88 -24 -213 198 -1164 -1164 139 -134 -1164 -47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 32 E= 3.9e-011 0.093750 0.718750 0.000000 0.187500 0.812500 0.000000 0.000000 0.187500 0.343750 0.625000 0.000000 0.031250 0.343750 0.593750 0.031250 0.031250 0.156250 0.343750 0.218750 0.281250 0.000000 0.968750 0.000000 0.031250 0.781250 0.031250 0.156250 0.031250 0.718750 0.218750 0.062500 0.000000 0.250000 0.750000 0.000000 0.000000 0.375000 0.281250 0.281250 0.062500 0.281250 0.437500 0.062500 0.218750 0.156250 0.781250 0.000000 0.062500 0.750000 0.125000 0.000000 0.125000 0.250000 0.406250 0.125000 0.218750 0.062500 0.937500 0.000000 0.000000 0.718750 0.093750 0.000000 0.187500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[CA][CA][CTG]CA[AC][CA][ACG][CAT]CA[CAT]CA -------------------------------------------------------------------------------- Time 9.73 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 20 llr = 224 E-value = 7.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :551:::2::21:31: pos.-specific C 72142:91:931a3:9 probability G 23:27217:16::25: matrix T 115429::a1:9:352 bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * * Relative 1.3 ** ** ** * Entropy 1.1 ** ** ** * (16.2 bits) 0.8 * ****** ** ** 0.6 * * ********* ** 0.4 * * ********* ** 0.2 ************* ** 0.0 ---------------- Multilevel CAATGTCGTCGTCCTC consensus GGTC A C AG sequence G A T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 1965 47 1.32e-09 TTGTCGTTGA CAACGTCGTCGTCCTC TAACTTCAAC 261748 124 2.31e-08 GCAGACGTAG CGTCGTCGTCCTCCTC ATTATCTTCG 28326 207 5.49e-08 GATTTCCTTT CATCGTCGTCATCGTC CATTGGTTCC 270376 446 5.49e-08 GATTTCCTTT CATCGTCGTCATCGTC CATTGGTTCC 268908 16 1.37e-07 GTTGCTTCAG CATGGTCATCGTCTGC ATTCACATCA 33663 239 3.80e-07 CAGCAATCCA CCATCTCGTCGTCATC AAGTGCGTTC 270301 219 3.80e-07 CAGCAATCCA CCATCTCGTCGTCATC AAGTGCGTTC 28521 427 2.34e-06 GCTTGCTGAA CAATGGCCTCCTCCGC TTCCGTTATG 25839 228 2.34e-06 ACCCATTTGA GGAGGGCGTCCTCCTC CAGGTGGAGG 262796 96 2.81e-06 CAAAGCTCGA GATTGTCATCGTCTGT GAACGGTGGT 24399 213 3.69e-06 TTCCAGATTC CATTTTCGTCGACATC ACCCGTACGA 36462 435 5.20e-06 AAGGCTGCAC GGAGGTGGTCCTCTTC CCTCCCTTCC 260974 141 5.66e-06 CCGATTTTGT GCACGTCCTCCTCTGC ATTGTCACCT 33000 338 9.01e-06 TTGAGAGGAC TGCTGTCGTCGTCAGT CATGCTGTTT 262849 412 9.72e-06 ACTGAAGATT CATCGGCGTTGCCCGC GCTTTTTCAT 12234 72 1.71e-05 GCACACGTCA CTTTTTCGTCACCAGC TTCGATAAAA 36208 381 1.96e-05 ATCTGCGTGA TGATGTGGTTGTCTGC TGACGTAATC 24082 154 1.96e-05 TTATCCCCTC CTCAGTCGTCGTCCGT CGTCGCTCGG 21081 432 1.96e-05 ATTTGCATCT CGTGCTCATGGTCGTC GTTGCATCTT 30747 192 2.09e-05 GGGGGGAATT CAACTTCATCATCGAC TACAACCGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1965 1.3e-09 46_[+2]_438 261748 2.3e-08 123_[+2]_361 28326 5.5e-08 206_[+2]_278 270376 5.5e-08 445_[+2]_39 268908 1.4e-07 15_[+2]_469 33663 3.8e-07 238_[+2]_246 270301 3.8e-07 218_[+2]_266 28521 2.3e-06 426_[+2]_58 25839 2.3e-06 227_[+2]_257 262796 2.8e-06 95_[+2]_389 24399 3.7e-06 212_[+2]_272 36462 5.2e-06 434_[+2]_50 260974 5.7e-06 140_[+2]_344 33000 9e-06 337_[+2]_147 262849 9.7e-06 411_[+2]_73 12234 1.7e-05 71_[+2]_413 36208 2e-05 380_[+2]_104 24082 2e-05 153_[+2]_331 21081 2e-05 431_[+2]_53 30747 2.1e-05 191_[+2]_293 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=20 1965 ( 47) CAACGTCGTCGTCCTC 1 261748 ( 124) CGTCGTCGTCCTCCTC 1 28326 ( 207) CATCGTCGTCATCGTC 1 270376 ( 446) CATCGTCGTCATCGTC 1 268908 ( 16) CATGGTCATCGTCTGC 1 33663 ( 239) CCATCTCGTCGTCATC 1 270301 ( 219) CCATCTCGTCGTCATC 1 28521 ( 427) CAATGGCCTCCTCCGC 1 25839 ( 228) GGAGGGCGTCCTCCTC 1 262796 ( 96) GATTGTCATCGTCTGT 1 24399 ( 213) CATTTTCGTCGACATC 1 36462 ( 435) GGAGGTGGTCCTCTTC 1 260974 ( 141) GCACGTCCTCCTCTGC 1 33000 ( 338) TGCTGTCGTCGTCAGT 1 262849 ( 412) CATCGGCGTTGCCCGC 1 12234 ( 72) CTTTTTCGTCACCAGC 1 36208 ( 381) TGATGTGGTTGTCTGC 1 24082 ( 154) CTCAGTCGTCGTCCGT 1 21081 ( 432) CGTGCTCATGGTCGTC 1 30747 ( 192) CAACTTCATCATCGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 9.84989 E= 7.2e-006 -1097 156 -20 -137 72 -66 38 -137 72 -125 -1097 80 -245 56 -20 63 -1097 -66 160 -79 -1097 -1097 -62 171 -1097 192 -120 -1097 -45 -125 160 -1097 -1097 -1097 -1097 195 -1097 184 -220 -137 -45 8 126 -1097 -245 -125 -1097 171 -1097 208 -1097 -1097 -13 34 -20 -5 -245 -1097 97 95 -1097 184 -1097 -79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 7.2e-006 0.000000 0.700000 0.200000 0.100000 0.450000 0.150000 0.300000 0.100000 0.450000 0.100000 0.000000 0.450000 0.050000 0.350000 0.200000 0.400000 0.000000 0.150000 0.700000 0.150000 0.000000 0.000000 0.150000 0.850000 0.000000 0.900000 0.100000 0.000000 0.200000 0.100000 0.700000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.850000 0.050000 0.100000 0.200000 0.250000 0.550000 0.000000 0.050000 0.100000 0.000000 0.850000 0.000000 1.000000 0.000000 0.000000 0.250000 0.300000 0.200000 0.250000 0.050000 0.000000 0.450000 0.500000 0.000000 0.850000 0.000000 0.150000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CG][AG][AT][TCG]GTC[GA]TC[GCA]TC[CATG][TG]C -------------------------------------------------------------------------------- Time 18.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 16 llr = 209 E-value = 2.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3::311:::4:33946311: pos.-specific C 32:13:4:::5:14:2:3:15 probability G 8213:633:a:344:3:1911 matrix T :3964317a:171:1143:84 bits 2.1 * 1.9 ** 1.7 * ** * 1.5 * ** * * Relative 1.3 * * ** * * Entropy 1.1 * * *** * * * (18.9 bits) 0.8 * ** * *** * * * *** 0.6 * ** * ***** * * *** 0.4 * **** ***** ** * *** 0.2 * ******************* 0.0 --------------------- Multilevel GATTTGCTTGCTGCAAAAGTC consensus CT GATGG AGAG GTC T sequence C A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 28326 151 3.08e-11 CTCGTTAAAA GATTTGCTTGCTGGAATCGTC ATCACCGACA 270376 390 3.08e-11 CTCGTTAAAA GATTTGCTTGCTGGAATCGTC ATCACCGACA 262796 122 1.78e-08 GAACGGTGGT GATTCTCTTGATAGAGATGTT TGACGTTGAT 33663 139 3.14e-08 AGTGCCATAC GTTTAGTGTGATACAAAAGTC TAGCCCTTCA 270301 119 3.14e-08 AGTGCCATAC GTTTAGTGTGATACAAAAGTC TAGCCCTTCA bd846 310 1.35e-07 CTCATCGTGT GTTTTTGTTGCTTCACTTGTT AGTCTCGTGG 260974 347 4.80e-07 CACACGGGAC CTTTTTCTTGCTCAACTTGTC GCAGCTGACG 12234 50 4.80e-07 TAGAACTTCA CAGTTGGGTGCTGCACACGTC ACTTTTTCGT 24082 116 8.61e-07 AAAAGTATGG CCTTTGATTGAGCAAAACGTT GCATTAGTTA 268908 354 1.09e-06 GGGTATCAAC GATGAGGTTGTGGCAGAGGTT GGCTATGAGA 22396 387 1.17e-06 AGCGCAACGA GTTGAACTTGAGAGAGAAGAC TTTAGTTGAA 1965 363 1.17e-06 TTCGCTCGGT GCTGCAGTTGCGGGAAACGCT GATTGAGAGA 30747 103 2.51e-06 TTGAGGCGGT GGTGCGGGTGAGGAATATGGT GGGCGGTGAT 31673 247 3.62e-06 AGTCACAGGT GCTTCGATTGCTGAAATTATG GGTAGAACCG 28521 160 4.06e-06 GAATATCGAT CGTCCTCTTGATTGATAAGTC ATTTTATGTT 262849 177 4.30e-06 GGACGAAGAC GGTGAGCGTGCTACTGTAGAT CGGTGCGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28326 3.1e-11 150_[+3]_329 270376 3.1e-11 389_[+3]_90 262796 1.8e-08 121_[+3]_358 33663 3.1e-08 138_[+3]_341 270301 3.1e-08 118_[+3]_361 bd846 1.3e-07 309_[+3]_170 260974 4.8e-07 346_[+3]_133 12234 4.8e-07 49_[+3]_430 24082 8.6e-07 115_[+3]_364 268908 1.1e-06 353_[+3]_126 22396 1.2e-06 386_[+3]_93 1965 1.2e-06 362_[+3]_117 30747 2.5e-06 102_[+3]_377 31673 3.6e-06 246_[+3]_233 28521 4.1e-06 159_[+3]_320 262849 4.3e-06 176_[+3]_303 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=16 28326 ( 151) GATTTGCTTGCTGGAATCGTC 1 270376 ( 390) GATTTGCTTGCTGGAATCGTC 1 262796 ( 122) GATTCTCTTGATAGAGATGTT 1 33663 ( 139) GTTTAGTGTGATACAAAAGTC 1 270301 ( 119) GTTTAGTGTGATACAAAAGTC 1 bd846 ( 310) GTTTTTGTTGCTTCACTTGTT 1 260974 ( 347) CTTTTTCTTGCTCAACTTGTC 1 12234 ( 50) CAGTTGGGTGCTGCACACGTC 1 24082 ( 116) CCTTTGATTGAGCAAAACGTT 1 268908 ( 354) GATGAGGTTGTGGCAGAGGTT 1 22396 ( 387) GTTGAACTTGAGAGAGAAGAC 1 1965 ( 363) GCTGCAGTTGCGGGAAACGCT 1 30747 ( 103) GGTGCGGGTGAGGAATATGGT 1 31673 ( 247) GCTTCGATTGCTGAAATTATG 1 28521 ( 160) CGTCCTCTTGATTGATAAGTC 1 262849 ( 177) GGTGAGCGTGCTACTGTAGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 10.643 E= 2.0e-003 -1064 8 170 -1064 19 -34 -30 27 -1064 -1064 -188 186 -1064 -192 44 127 19 40 -1064 53 -113 -1064 144 -5 -113 88 44 -105 -1064 -1064 44 141 -1064 -1064 -1064 195 -1064 -1064 212 -1064 68 108 -1064 -205 -1064 -1064 44 141 19 -92 93 -105 -13 66 70 -1064 178 -1064 -1064 -205 68 -34 12 -105 119 -1064 -1064 53 19 40 -188 27 -213 -1064 202 -1064 -113 -192 -188 153 -1064 108 -188 76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 2.0e-003 0.000000 0.250000 0.750000 0.000000 0.312500 0.187500 0.187500 0.312500 0.000000 0.000000 0.062500 0.937500 0.000000 0.062500 0.312500 0.625000 0.312500 0.312500 0.000000 0.375000 0.125000 0.000000 0.625000 0.250000 0.125000 0.437500 0.312500 0.125000 0.000000 0.000000 0.312500 0.687500 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.437500 0.500000 0.000000 0.062500 0.000000 0.000000 0.312500 0.687500 0.312500 0.125000 0.437500 0.125000 0.250000 0.375000 0.375000 0.000000 0.937500 0.000000 0.000000 0.062500 0.437500 0.187500 0.250000 0.125000 0.625000 0.000000 0.000000 0.375000 0.312500 0.312500 0.062500 0.312500 0.062500 0.000000 0.937500 0.000000 0.125000 0.062500 0.062500 0.750000 0.000000 0.500000 0.062500 0.437500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][AT]T[TG][TAC][GT][CG][TG]TG[CA][TG][GA][CGA]A[AG][AT][ACT]GT[CT] -------------------------------------------------------------------------------- Time 28.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12234 3.52e-06 49_[+3(4.80e-07)]_1_[+2(1.71e-05)]_\ 381_[+1(2.18e-05)]_16 1965 1.21e-10 46_[+2(1.32e-09)]_252_\ [+1(1.55e-06)]_32_[+3(1.17e-06)]_117 21081 3.11e-04 431_[+2(1.96e-05)]_16_\ [+1(5.53e-06)]_21 21821 3.12e-02 440_[+1(4.66e-05)]_44 22396 3.23e-03 386_[+3(1.17e-06)]_93 22768 1.69e-03 107_[+1(6.12e-07)]_377 24082 6.26e-07 115_[+3(8.61e-07)]_17_\ [+2(1.96e-05)]_53_[+1(1.55e-06)]_262 24399 8.59e-04 212_[+2(3.69e-06)]_237_\ [+1(3.96e-05)]_19 25839 5.82e-05 227_[+2(2.34e-06)]_174_\ [+1(4.95e-06)]_67 260953 4.63e-02 259_[+1(1.99e-05)]_225 260974 7.91e-07 140_[+2(5.66e-06)]_190_\ [+3(4.80e-07)]_33_[+1(3.08e-05)]_6_[+1(7.42e-05)]_35_[+1(1.25e-05)]_11 261748 3.55e-05 123_[+2(2.31e-08)]_361 262796 1.20e-07 9_[+1(8.61e-05)]_70_[+2(2.81e-06)]_\ 10_[+3(1.78e-08)]_358 262849 2.70e-06 176_[+3(4.30e-06)]_214_\ [+2(9.72e-06)]_55_[+1(3.17e-06)]_2 268908 2.84e-07 15_[+2(1.37e-07)]_3_[+1(7.42e-05)]_\ 303_[+3(1.09e-06)]_126 270301 1.49e-10 118_[+3(3.14e-08)]_79_\ [+2(3.80e-07)]_185_[+1(2.50e-07)]_65 270376 3.08e-14 389_[+3(3.08e-11)]_35_\ [+2(5.49e-08)]_23_[+1(2.15e-07)] 28326 3.08e-14 150_[+3(3.08e-11)]_35_\ [+2(5.49e-08)]_23_[+1(2.15e-07)]_239 28521 4.01e-06 129_[+1(2.18e-05)]_14_\ [+3(4.06e-06)]_246_[+2(2.34e-06)]_58 30747 1.21e-05 10_[+1(1.37e-05)]_76_[+3(2.51e-06)]_\ 68_[+2(2.09e-05)]_293 31673 4.16e-03 246_[+3(3.62e-06)]_233 32955 2.65e-03 127_[+1(4.43e-06)]_357 33000 9.53e-03 337_[+2(9.01e-06)]_147 3353 1.90e-01 477_[+1(5.05e-05)]_7 33663 1.49e-10 138_[+3(3.14e-08)]_79_\ [+2(3.80e-07)]_185_[+1(2.50e-07)]_45 34585 2.03e-01 181_[+1(5.46e-05)]_303 36208 7.97e-05 312_[+1(3.96e-05)]_41_\ [+3(7.97e-06)]_110 36462 2.41e-07 36_[+1(2.99e-09)]_253_\ [+1(4.30e-05)]_113_[+2(5.20e-06)]_50 6770 1.03e-01 33_[+1(1.37e-05)]_451 9352 6.40e-01 500 9485 1.22e-03 385_[+1(1.82e-07)]_99 bd846 4.33e-07 106_[+1(1.53e-07)]_187_\ [+3(1.35e-07)]_170 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************