******************************************************************************** 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/69/69.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 5850 1.0000 500 7957 1.0000 500 8011 1.0000 500 9394 1.0000 500 bd1319 1.0000 500 bd1339 1.0000 500 bd1360 1.0000 500 bd1380 1.0000 500 bd1441 1.0000 500 bd1645 1.0000 500 bd1720 1.0000 500 bd2088 1.0000 500 bd466 1.0000 500 bd467 1.0000 500 ThpsCp007 1.0000 500 ThpsCp010 1.0000 500 ThpsCp011 1.0000 500 ThpsCp046 1.0000 500 ThpsCp048 1.0000 500 ThpsCp050 1.0000 500 ThpsCp051 1.0000 500 ThpsCp055 1.0000 500 ThpsCp058 1.0000 500 ThpsCp059 1.0000 500 ThpsCp060 1.0000 500 ThpsCp062 1.0000 500 ThpsCp063 1.0000 500 ThpsCp064 1.0000 500 ThpsCp065 1.0000 500 ThpsCp066 1.0000 500 ThpsCp068 1.0000 500 ThpsCp069 1.0000 500 ThpsCp070 1.0000 500 ThpsCp071 1.0000 500 ThpsCp073 1.0000 500 ThpsCp076 1.0000 500 ThpsCp083 1.0000 500 ThpsCp088 1.0000 500 ThpsCp128 1.0000 500 ThpsCp133 1.0000 500 ThpsCp140 1.0000 500 ThpsCr003 1.0000 500 ThpsCr004 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/69/69.seqs.fa -oc motifs/69 -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= 43 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= 21500 N= 43 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.344 C 0.141 G 0.166 T 0.348 Background letter frequencies (from dataset with add-one prior applied): A 0.344 C 0.142 G 0.166 T 0.348 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 27 llr = 353 E-value = 1.2e-026 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :365:13311131:a219414 pos.-specific C 86::73233:1:17:38::31 probability G 21:4::23:9624::51:4:: matrix T ::4:36316:1533:::1175 bits 2.8 2.5 2.3 * 2.0 * Relative 1.7 * * * * Entropy 1.4 * * * ** * (18.8 bits) 1.1 ** * * ** * 0.8 ** ** ** ***** 0.6 ****** *** ******* 0.3 ****** **** ********* 0.0 --------------------- Multilevel CCAACTAGTGGTGCAGCAATT consensus ATGTCTAC ATT C GCA sequence GC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCp059 8 3.60e-12 TGAAATG CCAACCGGCGGTGCAGCAATA ATGCGCAATG bd467 7 3.60e-12 GAAATG CCAACCGGCGGTGCAGCAATA ATGCGCAATG ThpsCp010 106 1.55e-09 AGAAGATTCA CCTGCTACAGCTGCAGCAGCT TCTACTGGAT bd1360 26 1.55e-09 AGAAGATTCA CCTGCTACAGCTGCAGCAGCT TCTACTGGAT ThpsCr004 236 1.25e-08 CCGAGAAGGA CATACCTCTGGTGTACCAGTT ATCGTGCCAA ThpsCr003 238 1.25e-08 CCGAGAAGGA CATACCTCTGGTGTACCAGTT ATCGTGCCAA ThpsCp076 33 1.25e-08 CCGAGAAGGA CATACCTCTGGTGTACCAGTT ATCGTGCCAA ThpsCp055 119 9.19e-08 GCATTCTGGT CGTGCTCGTGCAGCAGCGGCT GGTTTCGAAA ThpsCp060 293 2.58e-07 TGCTGCTGTA CCAATTGTTGGGCCACCATTA GTTTTAGTTT bd466 281 2.58e-07 TGCTGCTGTA CCAATTGTTGGGCCACCATTA GTTTTAGTTT ThpsCp063 391 3.46e-07 CCGTTGGTTA GCAGTTCATGGATTAGCAATT CCAACGGTAT ThpsCp062 263 3.46e-07 CCGTTGGTTA GCAGTTCATGGATTAGCAATT CCAACGGTAT ThpsCp051 280 7.29e-07 AAAAATTAAA CCAACAAGCGGTACAAGAATA GAAGGTAAAA ThpsCp050 110 7.29e-07 AAAAATTAAA CCAACAAGCGGTACAAGAATA GAAGGTAAAA 5850 119 7.29e-07 TGGAGGAGTG GCAACTTATGTTTCAACAGTT GAAAGGTGAG ThpsCp066 213 1.34e-06 TGCTAAATGT CCAACAAACGGGTCATCATTA TACGGTTTAA ThpsCp046 186 1.59e-06 ATTTGAACCC CCAACCTACGGATTACAAATC CGTTGCTCTA bd1720 271 1.59e-06 ATTTGAACCC CCAACCTACGGATTACAAATC CGTTGCTCTA ThpsCp065 293 1.73e-06 TTTAGAAGAT CAAGCTGCTGATTTAGCAAAA TTCTTAGATT ThpsCp064 22 1.73e-06 TTTAGAAGAT CAAGCTGCTGATTTAGCAAAA TTCTTAGATT ThpsCp069 247 2.03e-06 GTTAGGATTA ACAATTTATGGTGCAGCTGCT TTTGGTCAAG ThpsCp133 301 2.21e-06 ATCGGGATTT CGTGCTCGTATGGCAACAGCT CAAGGAAGAA ThpsCp083 303 2.21e-06 ATCGGGATTT CGTGCTCGTATGGCAACAGCT CAAGGAAGAA ThpsCp070 213 3.03e-06 TTGCAAAAAT GATGTTAGAGGAACAGCAATA TCAATTAACA bd1380 212 3.03e-06 TTGCAAAAAT GATGTTAGAGGAACAGCAATA TCAATTAACA bd1645 402 4.12e-06 ATTCGGATTG CCATTCTCCGCCCCAGCCGCT TCTTCCAGCG ThpsCp007 53 6.88e-06 TACAAACCGT CCAGCTAATGAGCCAGGTTTC TACTTAGATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp059 3.6e-12 7_[+1]_472 bd467 3.6e-12 6_[+1]_473 ThpsCp010 1.5e-09 105_[+1]_374 bd1360 1.5e-09 25_[+1]_454 ThpsCr004 1.2e-08 235_[+1]_244 ThpsCr003 1.2e-08 237_[+1]_242 ThpsCp076 1.2e-08 32_[+1]_447 ThpsCp055 9.2e-08 118_[+1]_361 ThpsCp060 2.6e-07 292_[+1]_187 bd466 2.6e-07 280_[+1]_199 ThpsCp063 3.5e-07 390_[+1]_89 ThpsCp062 3.5e-07 262_[+1]_217 ThpsCp051 7.3e-07 279_[+1]_200 ThpsCp050 7.3e-07 109_[+1]_370 5850 7.3e-07 118_[+1]_361 ThpsCp066 1.3e-06 212_[+1]_267 ThpsCp046 1.6e-06 185_[+1]_294 bd1720 1.6e-06 270_[+1]_209 ThpsCp065 1.7e-06 292_[+1]_187 ThpsCp064 1.7e-06 21_[+1]_458 ThpsCp069 2e-06 246_[+1]_233 ThpsCp133 2.2e-06 300_[+1]_179 ThpsCp083 2.2e-06 302_[+1]_177 ThpsCp070 3e-06 212_[+1]_267 bd1380 3e-06 211_[+1]_268 bd1645 4.1e-06 401_[+1]_78 ThpsCp007 6.9e-06 52_[+1]_427 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=27 ThpsCp059 ( 8) CCAACCGGCGGTGCAGCAATA 1 bd467 ( 7) CCAACCGGCGGTGCAGCAATA 1 ThpsCp010 ( 106) CCTGCTACAGCTGCAGCAGCT 1 bd1360 ( 26) CCTGCTACAGCTGCAGCAGCT 1 ThpsCr004 ( 236) CATACCTCTGGTGTACCAGTT 1 ThpsCr003 ( 238) CATACCTCTGGTGTACCAGTT 1 ThpsCp076 ( 33) CATACCTCTGGTGTACCAGTT 1 ThpsCp055 ( 119) CGTGCTCGTGCAGCAGCGGCT 1 ThpsCp060 ( 293) CCAATTGTTGGGCCACCATTA 1 bd466 ( 281) CCAATTGTTGGGCCACCATTA 1 ThpsCp063 ( 391) GCAGTTCATGGATTAGCAATT 1 ThpsCp062 ( 263) GCAGTTCATGGATTAGCAATT 1 ThpsCp051 ( 280) CCAACAAGCGGTACAAGAATA 1 ThpsCp050 ( 110) CCAACAAGCGGTACAAGAATA 1 5850 ( 119) GCAACTTATGTTTCAACAGTT 1 ThpsCp066 ( 213) CCAACAAACGGGTCATCATTA 1 ThpsCp046 ( 186) CCAACCTACGGATTACAAATC 1 bd1720 ( 271) CCAACCTACGGATTACAAATC 1 ThpsCp065 ( 293) CAAGCTGCTGATTTAGCAAAA 1 ThpsCp064 ( 22) CAAGCTGCTGATTTAGCAAAA 1 ThpsCp069 ( 247) ACAATTTATGGTGCAGCTGCT 1 ThpsCp133 ( 301) CGTGCTCGTATGGCAACAGCT 1 ThpsCp083 ( 303) CGTGCTCGTATGGCAACAGCT 1 ThpsCp070 ( 213) GATGTTAGAGGAACAGCAATA 1 bd1380 ( 212) GATGTTAGAGGAACAGCAATA 1 bd1645 ( 402) CCATTCTCCGCCCCAGCCGCT 1 ThpsCp007 ( 53) CCAGCTAATGAGCCAGGTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20640 bayes= 10.146 E= 1.2e-026 -321 246 16 -1140 -41 215 -58 -1140 87 -1140 -1140 9 59 -1140 142 -323 -1140 231 -1140 -23 -163 107 -1140 77 -22 39 42 -23 -22 107 100 -223 -122 107 -1140 67 -221 -1140 248 -1140 -163 7 192 -165 -41 -193 42 47 -122 7 129 -23 -1140 224 -1140 -6 154 -1140 -1140 -1140 -89 87 164 -323 -221 253 -58 -1140 131 -193 -216 -223 37 -1140 129 -123 -221 87 -1140 94 24 -35 -1140 47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 1.2e-026 0.037037 0.777778 0.185185 0.000000 0.259259 0.629630 0.111111 0.000000 0.629630 0.000000 0.000000 0.370370 0.518519 0.000000 0.444444 0.037037 0.000000 0.703704 0.000000 0.296296 0.111111 0.296296 0.000000 0.592593 0.296296 0.185185 0.222222 0.296296 0.296296 0.296296 0.333333 0.074074 0.148148 0.296296 0.000000 0.555556 0.074074 0.000000 0.925926 0.000000 0.111111 0.148148 0.629630 0.111111 0.259259 0.037037 0.222222 0.481481 0.148148 0.148148 0.407407 0.296296 0.000000 0.666667 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.185185 0.259259 0.518519 0.037037 0.074074 0.814815 0.111111 0.000000 0.851852 0.037037 0.037037 0.074074 0.444444 0.000000 0.407407 0.148148 0.074074 0.259259 0.000000 0.666667 0.407407 0.111111 0.000000 0.481481 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[CA][AT][AG][CT][TC][ATG][GAC][TC]GG[TAG][GT][CT]A[GC]CA[AG][TC][TA] -------------------------------------------------------------------------------- Time 12.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 18 llr = 283 E-value = 2.6e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::13:14841:342:::11:: pos.-specific C 42:2:9:131a7443222618 probability G 388:::3::2:::26:34262 matrix T 3:15a:2226::22186313: bits 2.8 * 2.5 * * 2.3 * * 2.0 * * * * Relative 1.7 * * ** * Entropy 1.4 ** ** ** * (22.7 bits) 1.1 ** ** ** ** * 0.8 *** ** ** ** *** 0.6 *** ** ** *********** 0.3 ********************* 0.0 --------------------- Multilevel CGGTTCAAATCCACGTTGCGC consensus G A G C ACGC GTGTG sequence T C T T T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCp059 399 1.72e-10 CGGATTCCGT GGGTTCGAATCCCACTCTCGC CTTTTTATTT bd467 398 1.72e-10 CGGATTCCGT GGGTTCGAATCCCACTCTCGC CTTTTTATTT ThpsCp048 137 4.17e-10 TTTGTACCCA GGGTTCGAATCCCTGTTTCTC CTATTTTAAA ThpsCp065 438 6.34e-10 CTAATGATGG GGGTTCGATTCCCCCTGCCCG CTTTAGGTTA ThpsCp064 167 6.34e-10 CTAATGATGG GGGTTCGATTCCCCCTGCCCG CTTTAGGTTA ThpsCr004 67 7.29e-09 ACCTCGATGT CGGCTCATCGCATCCTGGGGC GGTAGTACGT ThpsCr003 69 7.29e-09 ACCTCGATGT CGGCTCATCGCATCCTGGGGC GGTAGTACGT ThpsCp060 64 9.04e-09 GGTGGTTAAT CCGTTCAATTCACCGTTGGTC AGCAAGTATG bd466 52 9.04e-09 GGTGGTTAAT CCGTTCAATTCACCGTTGGTC AGCAAGTATG ThpsCp058 408 3.02e-08 CGAAGGTCAA TGGTTCAAATCCATTCTCCGC TAGAAAATTT bd1339 395 3.02e-08 CGAAGGTCAA TGGTTCAAATCCATTCTCCGC TAGAAAATTT 5850 384 3.31e-08 GCCTGCATCA CCGCTAGTCTCCACGTTGCTC TGCCGCCGCT 7957 452 5.23e-08 CTCTCGTGTC CGTCTCACCTCCACGCGACGC CTCCAACAAA ThpsCp010 132 2.62e-07 CAGCTTCTAC TGGATCTACACCTGGTTGTGG TGTGATACGG bd1360 52 2.62e-07 CAGCTTCTAC TGGATCTACACCTGGTTGTGG TGTGATACGG 8011 285 5.23e-07 TCATACAGTA TGTATCAAAGCAAAGTCTCGC GAACAACTTG ThpsCp070 123 5.96e-07 ATAGTTTTTA CGAATCTAACCCAGGTTTATC ATCACGTATT bd1380 122 5.96e-07 ATAGTTTTTA CGAATCTAACCCAGGTTTATC ATCACGTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp059 1.7e-10 398_[+2]_81 bd467 1.7e-10 397_[+2]_82 ThpsCp048 4.2e-10 136_[+2]_343 ThpsCp065 6.3e-10 437_[+2]_42 ThpsCp064 6.3e-10 166_[+2]_313 ThpsCr004 7.3e-09 66_[+2]_413 ThpsCr003 7.3e-09 68_[+2]_411 ThpsCp060 9e-09 63_[+2]_416 bd466 9e-09 51_[+2]_428 ThpsCp058 3e-08 407_[+2]_72 bd1339 3e-08 394_[+2]_85 5850 3.3e-08 383_[+2]_96 7957 5.2e-08 451_[+2]_28 ThpsCp010 2.6e-07 131_[+2]_348 bd1360 2.6e-07 51_[+2]_428 8011 5.2e-07 284_[+2]_195 ThpsCp070 6e-07 122_[+2]_357 bd1380 6e-07 121_[+2]_358 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=18 ThpsCp059 ( 399) GGGTTCGAATCCCACTCTCGC 1 bd467 ( 398) GGGTTCGAATCCCACTCTCGC 1 ThpsCp048 ( 137) GGGTTCGAATCCCTGTTTCTC 1 ThpsCp065 ( 438) GGGTTCGATTCCCCCTGCCCG 1 ThpsCp064 ( 167) GGGTTCGATTCCCCCTGCCCG 1 ThpsCr004 ( 67) CGGCTCATCGCATCCTGGGGC 1 ThpsCr003 ( 69) CGGCTCATCGCATCCTGGGGC 1 ThpsCp060 ( 64) CCGTTCAATTCACCGTTGGTC 1 bd466 ( 52) CCGTTCAATTCACCGTTGGTC 1 ThpsCp058 ( 408) TGGTTCAAATCCATTCTCCGC 1 bd1339 ( 395) TGGTTCAAATCCATTCTCCGC 1 5850 ( 384) CCGCTAGTCTCCACGTTGCTC 1 7957 ( 452) CGTCTCACCTCCACGCGACGC 1 ThpsCp010 ( 132) TGGATCTACACCTGGTTGTGG 1 bd1360 ( 52) TGGATCTACACCTGGTTGTGG 1 8011 ( 285) TGTATCAAAGCAAAGTCTCGC 1 ThpsCp070 ( 123) CGAATCTAACCCAGGTTTATC 1 bd1380 ( 122) CGAATCTAACCCAGGTTTATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20640 bayes= 10.2964 E= 2.6e-024 -1081 165 74 -32 -1081 24 232 -1081 -163 -1081 222 -165 -31 65 -1081 52 -1081 -1081 -1081 152 -263 274 -1081 -1081 37 -1081 100 -65 118 -135 -1081 -106 37 124 -1081 -65 -163 -35 0 81 -1081 282 -1081 -1081 -31 235 -1081 -1081 18 146 -1081 -65 -105 165 42 -106 -1081 124 174 -165 -1081 24 -1081 126 -1081 24 74 67 -263 65 123 -6 -163 197 42 -165 -1081 -35 174 -6 -1081 246 42 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 2.6e-024 0.000000 0.444444 0.277778 0.277778 0.000000 0.166667 0.833333 0.000000 0.111111 0.000000 0.777778 0.111111 0.277778 0.222222 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.055556 0.944444 0.000000 0.000000 0.444444 0.000000 0.333333 0.222222 0.777778 0.055556 0.000000 0.166667 0.444444 0.333333 0.000000 0.222222 0.111111 0.111111 0.166667 0.611111 0.000000 1.000000 0.000000 0.000000 0.277778 0.722222 0.000000 0.000000 0.388889 0.388889 0.000000 0.222222 0.166667 0.444444 0.222222 0.166667 0.000000 0.333333 0.555556 0.111111 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.277778 0.555556 0.055556 0.222222 0.388889 0.333333 0.111111 0.555556 0.222222 0.111111 0.000000 0.111111 0.555556 0.333333 0.000000 0.777778 0.222222 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CGT]GG[TAC]TC[AGT]A[ACT]TC[CA][ACT][CG][GC]T[TG][GTC][CG][GT][CG] -------------------------------------------------------------------------------- Time 25.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 26 llr = 334 E-value = 2.4e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:35717228:::166352 pos.-specific C ::::12:4355:561642::: probability G 624a6:35:2214413::53: matrix T 473::31:11111:8::2128 bits 2.8 2.5 * 2.3 * 2.0 * Relative 1.7 * * Entropy 1.4 * * * (18.6 bits) 1.1 * * * ** ** 0.8 ** ** * ******* * 0.6 ** ** *********** *** 0.3 ********************* 0.0 --------------------- Multilevel GTGGGAAGACCACCTCAAGAT consensus TGT ATGCCGA GG GCTAG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCr004 320 7.08e-13 AAGCATCTAA GTGGGAAGCCCACCTCAAGAT AAGTATTCTC ThpsCr003 322 7.08e-13 AAGCATCTAA GTGGGAAGCCCACCTCAAGAT AAGTATTCTC ThpsCp140 23 7.08e-13 AAGCATCTAA GTGGGAAGCCCACCTCAAGAT AAGTATTCTC ThpsCp076 117 7.08e-13 AAGCATCTAA GTGGGAAGCCCACCTCAAGAT AAGTATTCTC ThpsCp064 386 7.72e-09 ATATGATGTT TTTGGAACACCACGTCCTAAT GAATACTTTA ThpsCp063 207 7.72e-09 ATATGATGTT TTTGGAACACCACGTCCTAAT GAATACTTTA ThpsCp062 79 7.72e-09 ATATGATGTT TTTGGAACACCACGTCCTAAT GAATACTTTA 7957 80 5.06e-07 TGGTGATGAC GTCGGTGCCGAAGGTGATGGT GATGACGTTG ThpsCp046 221 1.06e-06 GCTCTACCGT TGAGCTACACCAGCTGCCTAT CTTATAAGAT bd1720 306 1.06e-06 GCTCTACCGT TGAGCTACACCAGCTGCCTAT CTTATAAGAT ThpsCp070 367 1.27e-06 TAATCGTATA TTTGATAGCCGAGGTCAAGTA TTAACGAAAA bd1380 366 1.27e-06 TAATCGTATA TTTGATAGCCGAGGTCAAGTA TTAACGAAAA ThpsCp011 33 1.38e-06 TTGCATTTTA GTAGGCGAAAATGCTCAAGGT GAATTTTATT bd1319 16 1.38e-06 TTGCATTTTA GTAGGCGAAAATGCTCAAGGT GAATTTTATT ThpsCp048 248 1.64e-06 TGTAGTTCAA TTGGTTAGAGCACCGCCCTGT CACGGCGGAA bd1645 25 1.79e-06 GCTGATGGAC GGTGATGGATCGCCGGAAGGT GTGGTGTCTG ThpsCp058 384 2.11e-06 TGGTAGCTCG TTGGGCTCATAACCCGAAGGT CAATGGTTCA bd1339 371 2.11e-06 TGGTAGCTCG TTGGGCTCATAACCCGAAGGT CAATGGTTCA ThpsCp060 332 3.69e-06 TTTACGTGGT GGTGAAAGTGTAGGTCAAAGT ACGTTAACTC bd466 320 3.69e-06 TTTACGTGGT GGTGAAAGTGTAGGTCAAAGT ACGTTAACTC ThpsCp007 89 3.99e-06 AGATCGTACA GAAGGCGCAGGTCGTCAAGTT ATCTACAGTA ThpsCp133 22 4.30e-06 CTGATATTGC GTGGAAAGAACATCTACAAAA AATTGCATTA ThpsCp083 24 4.30e-06 CTGATATTGC GTGGAAAGAACATCTACAAAA AATTGCATTA 8011 43 5.00e-06 ATTTGGAGGA GGGGGAGGAGGAGGAACCAAT GACGTTTGGG 5850 461 5.79e-06 CAAGTGTCAA GTAGGTGCACCATCTCATCTC GCCTCATGTC ThpsCp066 12 2.04e-05 TAAACCAATT GTTGATAAAAAGCCTGCTAAT AATCCAATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCr004 7.1e-13 319_[+3]_160 ThpsCr003 7.1e-13 321_[+3]_158 ThpsCp140 7.1e-13 22_[+3]_457 ThpsCp076 7.1e-13 116_[+3]_363 ThpsCp064 7.7e-09 385_[+3]_94 ThpsCp063 7.7e-09 206_[+3]_273 ThpsCp062 7.7e-09 78_[+3]_401 7957 5.1e-07 79_[+3]_400 ThpsCp046 1.1e-06 220_[+3]_259 bd1720 1.1e-06 305_[+3]_174 ThpsCp070 1.3e-06 366_[+3]_113 bd1380 1.3e-06 365_[+3]_114 ThpsCp011 1.4e-06 32_[+3]_447 bd1319 1.4e-06 15_[+3]_464 ThpsCp048 1.6e-06 247_[+3]_232 bd1645 1.8e-06 24_[+3]_455 ThpsCp058 2.1e-06 383_[+3]_96 bd1339 2.1e-06 370_[+3]_109 ThpsCp060 3.7e-06 331_[+3]_148 bd466 3.7e-06 319_[+3]_160 ThpsCp007 4e-06 88_[+3]_391 ThpsCp133 4.3e-06 21_[+3]_458 ThpsCp083 4.3e-06 23_[+3]_456 8011 5e-06 42_[+3]_437 5850 5.8e-06 460_[+3]_19 ThpsCp066 2e-05 11_[+3]_468 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=26 ThpsCr004 ( 320) GTGGGAAGCCCACCTCAAGAT 1 ThpsCr003 ( 322) GTGGGAAGCCCACCTCAAGAT 1 ThpsCp140 ( 23) GTGGGAAGCCCACCTCAAGAT 1 ThpsCp076 ( 117) GTGGGAAGCCCACCTCAAGAT 1 ThpsCp064 ( 386) TTTGGAACACCACGTCCTAAT 1 ThpsCp063 ( 207) TTTGGAACACCACGTCCTAAT 1 ThpsCp062 ( 79) TTTGGAACACCACGTCCTAAT 1 7957 ( 80) GTCGGTGCCGAAGGTGATGGT 1 ThpsCp046 ( 221) TGAGCTACACCAGCTGCCTAT 1 bd1720 ( 306) TGAGCTACACCAGCTGCCTAT 1 ThpsCp070 ( 367) TTTGATAGCCGAGGTCAAGTA 1 bd1380 ( 366) TTTGATAGCCGAGGTCAAGTA 1 ThpsCp011 ( 33) GTAGGCGAAAATGCTCAAGGT 1 bd1319 ( 16) GTAGGCGAAAATGCTCAAGGT 1 ThpsCp048 ( 248) TTGGTTAGAGCACCGCCCTGT 1 bd1645 ( 25) GGTGATGGATCGCCGGAAGGT 1 ThpsCp058 ( 384) TTGGGCTCATAACCCGAAGGT 1 bd1339 ( 371) TTGGGCTCATAACCCGAAGGT 1 ThpsCp060 ( 332) GGTGAAAGTGTAGGTCAAAGT 1 bd466 ( 320) GGTGAAAGTGTAGGTCAAAGT 1 ThpsCp007 ( 89) GAAGGCGCAGGTCGTCAAGTT 1 ThpsCp133 ( 22) GTGGAAAGAACATCTACAAAA 1 ThpsCp083 ( 24) GTGGAAAGAACATCTACAAAA 1 8011 ( 43) GGGGGAGGAGGAGGAACCAAT 1 5850 ( 461) GTAGGTGCACCATCTCATCTC 1 ThpsCp066 ( 12) GTTGATAAAAAGCCTGCTAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20640 bayes= 10.162 E= 2.4e-020 -1134 -1134 189 14 -316 -1134 47 107 -58 -188 121 -1 -1134 -1134 259 -1134 -16 -88 179 -317 42 44 -1134 -1 93 -1134 69 -218 -158 144 159 -1134 93 93 -1134 -218 -84 171 47 -159 -58 193 -11 -218 123 -1134 -111 -159 -1134 182 121 -159 -1134 212 121 -1134 -316 -88 -111 121 -158 212 69 -1134 84 144 -1134 -1134 84 12 -1134 -59 1 -188 159 -159 54 -1134 106 -118 -116 -188 -1134 121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 2.4e-020 0.000000 0.000000 0.615385 0.384615 0.038462 0.000000 0.230769 0.730769 0.230769 0.038462 0.384615 0.346154 0.000000 0.000000 1.000000 0.000000 0.307692 0.076923 0.576923 0.038462 0.461538 0.192308 0.000000 0.346154 0.653846 0.000000 0.269231 0.076923 0.115385 0.384615 0.500000 0.000000 0.653846 0.269231 0.000000 0.076923 0.192308 0.461538 0.230769 0.115385 0.230769 0.538462 0.153846 0.076923 0.807692 0.000000 0.076923 0.115385 0.000000 0.500000 0.384615 0.115385 0.000000 0.615385 0.384615 0.000000 0.038462 0.076923 0.076923 0.807692 0.115385 0.615385 0.269231 0.000000 0.615385 0.384615 0.000000 0.000000 0.615385 0.153846 0.000000 0.230769 0.346154 0.038462 0.500000 0.115385 0.500000 0.000000 0.346154 0.153846 0.153846 0.038462 0.000000 0.807692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][TG][GTA]G[GA][AT][AG][GC][AC][CG][CA]A[CG][CG]T[CG][AC][AT][GA][AG]T -------------------------------------------------------------------------------- Time 37.92 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5850 5.19e-09 118_[+1(7.29e-07)]_244_\ [+2(3.31e-08)]_56_[+3(5.79e-06)]_19 7957 1.20e-07 79_[+3(5.06e-07)]_77_[+3(2.43e-05)]_\ 253_[+2(5.23e-08)]_28 8011 1.15e-05 42_[+3(5.00e-06)]_221_\ [+2(5.23e-07)]_123_[+3(4.22e-05)]_51 9394 9.21e-02 331_[+3(7.97e-05)]_148 bd1319 5.66e-03 15_[+3(1.38e-06)]_464 bd1339 1.82e-06 370_[+3(2.11e-06)]_3_[+2(3.02e-08)]_\ 85 bd1360 7.76e-09 25_[+1(1.55e-09)]_5_[+2(2.62e-07)]_\ 428 bd1380 6.76e-08 121_[+2(5.96e-07)]_69_\ [+1(3.03e-06)]_133_[+3(1.27e-06)]_114 bd1441 7.52e-01 500 bd1645 4.03e-05 24_[+3(1.79e-06)]_356_\ [+1(4.12e-06)]_78 bd1720 3.06e-05 270_[+1(1.59e-06)]_14_\ [+3(1.06e-06)]_174 bd2088 8.92e-01 500 bd466 3.92e-10 51_[+2(9.04e-09)]_208_\ [+1(2.58e-07)]_18_[+3(3.69e-06)]_24_[+1(8.63e-05)]_115 bd467 7.87e-14 6_[+1(3.60e-12)]_370_[+2(1.72e-10)]_\ 82 ThpsCp007 1.02e-04 52_[+1(6.88e-06)]_15_[+3(3.99e-06)]_\ 391 ThpsCp010 7.76e-09 105_[+1(1.55e-09)]_5_[+2(2.62e-07)]_\ 348 ThpsCp011 5.66e-03 32_[+3(1.38e-06)]_447 ThpsCp046 3.06e-05 185_[+1(1.59e-06)]_14_\ [+3(1.06e-06)]_259 ThpsCp048 1.20e-08 23_[+2(7.91e-05)]_92_[+2(4.17e-10)]_\ 90_[+3(1.64e-06)]_232 ThpsCp050 2.90e-03 109_[+1(7.29e-07)]_370 ThpsCp051 1.17e-02 279_[+1(7.29e-07)]_200 ThpsCp055 1.27e-03 118_[+1(9.19e-08)]_361 ThpsCp058 1.82e-06 383_[+3(2.11e-06)]_3_[+2(3.02e-08)]_\ 72 ThpsCp059 7.87e-14 7_[+1(3.60e-12)]_370_[+2(1.72e-10)]_\ 81 ThpsCp060 3.92e-10 63_[+2(9.04e-09)]_208_\ [+1(2.58e-07)]_18_[+3(3.69e-06)]_24_[+1(8.63e-05)]_103 ThpsCp062 8.00e-08 78_[+3(7.72e-09)]_163_\ [+1(3.46e-07)]_217 ThpsCp063 8.00e-08 71_[+3(1.01e-05)]_114_\ [+3(7.72e-09)]_163_[+1(3.46e-07)]_89 ThpsCp064 5.93e-13 21_[+1(1.73e-06)]_124_\ [+2(6.34e-10)]_63_[+3(1.01e-05)]_114_[+3(7.72e-09)]_94 ThpsCp065 6.70e-10 292_[+1(1.73e-06)]_124_\ [+2(6.34e-10)]_42 ThpsCp066 4.95e-04 11_[+3(2.04e-05)]_180_\ [+1(1.34e-06)]_267 ThpsCp068 7.77e-01 500 ThpsCp069 3.96e-03 246_[+1(2.03e-06)]_233 ThpsCp070 6.76e-08 122_[+2(5.96e-07)]_69_\ [+1(3.03e-06)]_133_[+3(1.27e-06)]_113 ThpsCp071 2.88e-01 500 ThpsCp073 8.85e-01 500 ThpsCp076 1.01e-12 32_[+1(1.25e-08)]_63_[+3(7.08e-13)]_\ 363 ThpsCp083 2.01e-04 23_[+3(4.30e-06)]_258_\ [+1(2.21e-06)]_177 ThpsCp088 8.13e-01 500 ThpsCp128 7.52e-01 500 ThpsCp133 2.01e-04 21_[+3(4.30e-06)]_258_\ [+1(2.21e-06)]_179 ThpsCp140 1.88e-08 22_[+3(7.08e-13)]_457 ThpsCr003 7.99e-18 68_[+2(7.29e-09)]_148_\ [+1(1.25e-08)]_63_[+3(7.08e-13)]_158 ThpsCr004 7.99e-18 66_[+2(7.29e-09)]_148_\ [+1(1.25e-08)]_63_[+3(7.08e-13)]_160 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************