******************************************************************************** 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/40/40.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ThpsCp093 1.0000 500 ThpsCp095 1.0000 500 ThpsCp096 1.0000 500 ThpsCp097 1.0000 500 ThpsCp098 1.0000 500 ThpsCp099 1.0000 500 ThpsCp100 1.0000 500 ThpsCp101 1.0000 500 ThpsCp102 1.0000 500 ThpsCp103 1.0000 500 ThpsCp104 1.0000 500 ThpsCp105 1.0000 500 ThpsCp106 1.0000 500 ThpsCp107 1.0000 500 ThpsCp108 1.0000 500 ThpsCp109 1.0000 500 ThpsCp110 1.0000 500 ThpsCp111 1.0000 500 ThpsCp112 1.0000 500 ThpsCp113 1.0000 500 ThpsCp114 1.0000 500 ThpsCp115 1.0000 500 ThpsCp116 1.0000 500 ThpsCp117 1.0000 500 ThpsCp118 1.0000 500 ThpsCp119 1.0000 500 ThpsCp120 1.0000 500 ThpsCp121 1.0000 500 ThpsCp122 1.0000 500 ThpsCp124 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/40/40.seqs.fa -oc motifs/40 -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 0.385 C 0.136 G 0.164 T 0.315 Background letter frequencies (from dataset with add-one prior applied): A 0.385 C 0.136 G 0.164 T 0.315 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 24 llr = 328 E-value = 1.8e-029 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :353:1::2::32573:1::5 pos.-specific C 331:2:14:9::14:33:242 probability G 74:61:93:19:5::32:34: matrix T ::5179:38:17213:59523 bits 2.9 2.6 2.3 * * 2.0 * * Relative 1.7 * ** Entropy 1.4 * * ** (19.7 bits) 1.2 * ** ** * 0.9 * ******** ** * 0.6 ** ********** ****** 0.3 ********************* 0.0 --------------------- Multilevel GGAGTTGCTCGTGAAATTTCA consensus CATA G AACTCC GGT sequence C T T GG CTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCp105 60 6.52e-10 TGTACCCGAA GAAGTTGCTCGTGCTGCTTTC AATTTAGCAG ThpsCp104 433 6.52e-10 TGTACCCGAA GAAGTTGCTCGTGCTGCTTTC AATTTAGCAG ThpsCp097 100 6.52e-10 GCGTCAAAAA GGAACTGGTCGTGCACGTGCC GGATCAAGCC ThpsCp108 180 7.74e-10 TGTATTTGGT CCTGTTGCTCGTGAAATTCGC GATAAGAATT ThpsCp107 446 7.74e-10 TGTATTTGGT CCTGTTGCTCGTGAAATTCGC GATAAGAATT ThpsCp113 270 5.90e-08 TATTGCTGGT GGTGCTGTTCGAACAGTTTTA GAAGTTGCTG ThpsCp112 443 6.58e-08 AGCTTTAGCC GATGGCGCTCGAGCAGGTGGT CTACAATTTT ThpsCp115 260 9.07e-08 AATTTTAGTT GGTGTTGTTCTTGATATTTCA CGTGAAATGA ThpsCp114 381 9.07e-08 AATTTTAGTT GGTGTTGTTCTTGATATTTCA CGTGAAATGA ThpsCp099 92 1.01e-07 CCGTGGGGGC CAAATTGTTCGTTCAGCTGGT ACATCAGCAA ThpsCp095 192 1.12e-07 TACAATTGAT GGTGTTGTGCGAAAACCTTCT GCATTTGTAA ThpsCp121 71 1.24e-07 TATTAAATTA GGTGTTGCACGATTACTTTGT AAAATGGAAC ThpsCp120 339 1.24e-07 TATTAAATTA GGTGTTGCACGATTACTTTGT AAAATGGAAC ThpsCp110 465 1.67e-07 AAAGTCTCTT GGAATTGGTGGTGAAGTTTTA TGTTATATTT ThpsCp103 280 2.03e-07 AGATAGGGTT GCATTTCGTCGTGCAATTCGA GAAGCATTAC ThpsCp124 235 7.17e-07 AACTAAAGAA GAAGGTGGTCGTCATACGCCA TTCTTTACAG ThpsCp096 419 7.79e-07 TGTTAAAGGA GCCGTTCCTGGAAAACCTGGA AACTTGCTTA ThpsCp100 76 8.46e-07 AGGTAGAACT CCCATTGGTCGTACACGACCT TTAACTCCAT ThpsCp111 198 1.08e-06 TCTTACATTA CAAGGTGTTGGTTATCGTGCA AGTGTTCAAG ThpsCp117 330 1.17e-06 TAAAGGTCAA GGTTCAGGACGTGAAACTGCA ATCCGATCAA ThpsCp106 448 2.31e-06 GAAGCGTTGG TCAGTTGCTCGAATTATTTCA AGATCATCTT ThpsCp122 405 4.03e-06 TGTTCGATAC CATATTGTTCGTGGAGCATTA GATAGTGGTG ThpsCp119 153 4.61e-06 CCATGTTTTT GAACCAGGACGTCCAGGTTCA TCATTAAAAC ThpsCp098 379 4.61e-06 AAAGAAAAAA CGAATTGGTCAATATCTTGGT TGGAAAGCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp105 6.5e-10 59_[+1]_420 ThpsCp104 6.5e-10 432_[+1]_47 ThpsCp097 6.5e-10 99_[+1]_380 ThpsCp108 7.7e-10 179_[+1]_300 ThpsCp107 7.7e-10 445_[+1]_34 ThpsCp113 5.9e-08 269_[+1]_210 ThpsCp112 6.6e-08 442_[+1]_37 ThpsCp115 9.1e-08 259_[+1]_220 ThpsCp114 9.1e-08 380_[+1]_99 ThpsCp099 1e-07 91_[+1]_388 ThpsCp095 1.1e-07 191_[+1]_288 ThpsCp121 1.2e-07 70_[+1]_409 ThpsCp120 1.2e-07 338_[+1]_141 ThpsCp110 1.7e-07 464_[+1]_15 ThpsCp103 2e-07 279_[+1]_200 ThpsCp124 7.2e-07 234_[+1]_245 ThpsCp096 7.8e-07 418_[+1]_61 ThpsCp100 8.5e-07 75_[+1]_404 ThpsCp111 1.1e-06 197_[+1]_282 ThpsCp117 1.2e-06 329_[+1]_150 ThpsCp106 2.3e-06 447_[+1]_32 ThpsCp122 4e-06 404_[+1]_75 ThpsCp119 4.6e-06 152_[+1]_327 ThpsCp098 4.6e-06 378_[+1]_101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=24 ThpsCp105 ( 60) GAAGTTGCTCGTGCTGCTTTC 1 ThpsCp104 ( 433) GAAGTTGCTCGTGCTGCTTTC 1 ThpsCp097 ( 100) GGAACTGGTCGTGCACGTGCC 1 ThpsCp108 ( 180) CCTGTTGCTCGTGAAATTCGC 1 ThpsCp107 ( 446) CCTGTTGCTCGTGAAATTCGC 1 ThpsCp113 ( 270) GGTGCTGTTCGAACAGTTTTA 1 ThpsCp112 ( 443) GATGGCGCTCGAGCAGGTGGT 1 ThpsCp115 ( 260) GGTGTTGTTCTTGATATTTCA 1 ThpsCp114 ( 381) GGTGTTGTTCTTGATATTTCA 1 ThpsCp099 ( 92) CAAATTGTTCGTTCAGCTGGT 1 ThpsCp095 ( 192) GGTGTTGTGCGAAAACCTTCT 1 ThpsCp121 ( 71) GGTGTTGCACGATTACTTTGT 1 ThpsCp120 ( 339) GGTGTTGCACGATTACTTTGT 1 ThpsCp110 ( 465) GGAATTGGTGGTGAAGTTTTA 1 ThpsCp103 ( 280) GCATTTCGTCGTGCAATTCGA 1 ThpsCp124 ( 235) GAAGGTGGTCGTCATACGCCA 1 ThpsCp096 ( 419) GCCGTTCCTGGAAAACCTGGA 1 ThpsCp100 ( 76) CCCATTGGTCGTACACGACCT 1 ThpsCp111 ( 198) CAAGGTGTTGGTTATCGTGCA 1 ThpsCp117 ( 330) GGTTCAGGACGTGAAACTGCA 1 ThpsCp106 ( 448) TCAGTTGCTCGAATTATTTCA 1 ThpsCp122 ( 405) CATATTGTTCGTGGAGCATTA 1 ThpsCp119 ( 153) GAACCAGGACGTCCAGGTTCA 1 ThpsCp098 ( 379) CGAATTGGTCAATATCTTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 10.3272 E= 1.8e-029 -1123 110 202 -291 -21 88 134 -1123 25 -71 -1123 54 -62 -171 193 -191 -1123 29 -39 117 -221 -171 -1123 148 -1123 -71 248 -1123 -1123 146 102 -11 -121 -1123 -198 133 -1123 268 -39 -1123 -320 -1123 241 -191 -21 -1123 -1123 108 -89 -71 160 -59 25 146 -198 -133 79 -1123 -1123 8 -21 129 102 -1123 -1123 129 34 54 -221 -1123 -198 148 -1123 61 83 67 -1123 161 119 -59 38 61 -1123 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 1.8e-029 0.000000 0.291667 0.666667 0.041667 0.333333 0.250000 0.416667 0.000000 0.458333 0.083333 0.000000 0.458333 0.250000 0.041667 0.625000 0.083333 0.000000 0.166667 0.125000 0.708333 0.083333 0.041667 0.000000 0.875000 0.000000 0.083333 0.916667 0.000000 0.000000 0.375000 0.333333 0.291667 0.166667 0.000000 0.041667 0.791667 0.000000 0.875000 0.125000 0.000000 0.041667 0.000000 0.875000 0.083333 0.333333 0.000000 0.000000 0.666667 0.208333 0.083333 0.500000 0.208333 0.458333 0.375000 0.041667 0.125000 0.666667 0.000000 0.000000 0.333333 0.333333 0.333333 0.333333 0.000000 0.000000 0.333333 0.208333 0.458333 0.083333 0.000000 0.041667 0.875000 0.000000 0.208333 0.291667 0.500000 0.000000 0.416667 0.375000 0.208333 0.500000 0.208333 0.000000 0.291667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC][GAC][AT][GA]TTG[CGT]TCG[TA][GAT][AC][AT][ACG][TCG]T[TGC][CGT][ATC] -------------------------------------------------------------------------------- Time 7.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 18 llr = 245 E-value = 4.2e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1::2::1:864911:3397: pos.-specific C :11122::1::3:13332:18 probability G :88365374131:73234:22 matrix T a116:37252221136111:: bits 2.9 2.6 2.3 2.0 * Relative 1.7 * * * Entropy 1.4 *** * (19.6 bits) 1.2 *** * ** * * 0.9 ********* ** * * * 0.6 ********** **** **** 0.3 ********************* 0.0 --------------------- Multilevel TGGTGGTGTAAAAGCTAGAAC consensus GATGTG GC GCGA G sequence C T T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCp100 54 2.76e-10 ATCATCCACA TGGGGGTGGTGAAGGTAGAAC TCCCATTGGT ThpsCp099 331 2.76e-10 ATCATCCACA TGGGGGTGGTGAAGGTAGAAC TCCCATTGGT ThpsCp121 34 8.46e-10 TTGTAAGAGG TGGTGGTTTAACAGGCCAAAC TGATTCTATT ThpsCp120 302 8.46e-10 TTGTAAGAGG TGGTGGTTTAACAGGCCAAAC TGATTCTATT ThpsCp122 431 1.40e-08 CATTAGATAG TGGTGGGGTTAAAGACCGAAC ACAAAGACGT ThpsCp113 80 1.08e-07 ATGGAAAAGT TGGCGTTGGAGTAGGGAAAGC TGAAGATGTT ThpsCp105 8 2.10e-07 ATTGGGT TGCTACGGTAAAACCGGGAAC AATTTTATTT ThpsCp104 381 2.10e-07 ACTATTGGGT TGCTACGGTAAAACCGGGAAC AATTTTATTT ThpsCp115 91 3.61e-07 TCCCTGGTGT TAGGCCTGGATTAGCTACAAC ATTTTATTTA ThpsCp114 212 3.61e-07 TCCCTGGTGT TAGGCCTGGATTAGCTACAAC ATTTTATTTA ThpsCp097 150 4.29e-07 TATGGAAAGG TGGTGGTGTAATATTTGGTCC AAAGCCTAAA ThpsCp096 283 6.54e-07 CAGGGTCAAT TGGTATGGGAACAAGCCCAGG TCGTGTTTTA ThpsCp124 27 7.09e-07 TAGAGATTGT TGGTGTTGGGGATACTCAAAC AACAACTATT ThpsCp106 288 7.69e-07 TGCAAAAAAC TGTGGTTGTAAAAGTTGAAAG CAGATATCCA ThpsCp093 187 9.03e-07 GAAAAAAAAC TGGGGTGGCAGGATTCGAACC TACGAATGGC ThpsCp103 251 2.58e-06 ATAGCTGATC TTGTAGTTCAACAGTTGGAAG ATAGGGTTGC ThpsCp109 159 3.40e-06 TTCGAGATTT TCGTGGTTTATCTGTTAGAAG TTTTGATAAA ThpsCp112 421 4.74e-06 ACTTGTATCA TGGTCGTATAAAAGCTTTAGC CGATGGCGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp100 2.8e-10 53_[+2]_426 ThpsCp099 2.8e-10 330_[+2]_149 ThpsCp121 8.5e-10 33_[+2]_446 ThpsCp120 8.5e-10 301_[+2]_178 ThpsCp122 1.4e-08 430_[+2]_49 ThpsCp113 1.1e-07 79_[+2]_400 ThpsCp105 2.1e-07 7_[+2]_472 ThpsCp104 2.1e-07 380_[+2]_99 ThpsCp115 3.6e-07 90_[+2]_389 ThpsCp114 3.6e-07 211_[+2]_268 ThpsCp097 4.3e-07 149_[+2]_330 ThpsCp096 6.5e-07 282_[+2]_197 ThpsCp124 7.1e-07 26_[+2]_453 ThpsCp106 7.7e-07 287_[+2]_192 ThpsCp093 9e-07 186_[+2]_293 ThpsCp103 2.6e-06 250_[+2]_229 ThpsCp109 3.4e-06 158_[+2]_321 ThpsCp112 4.7e-06 420_[+2]_59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=18 ThpsCp100 ( 54) TGGGGGTGGTGAAGGTAGAAC 1 ThpsCp099 ( 331) TGGGGGTGGTGAAGGTAGAAC 1 ThpsCp121 ( 34) TGGTGGTTTAACAGGCCAAAC 1 ThpsCp120 ( 302) TGGTGGTTTAACAGGCCAAAC 1 ThpsCp122 ( 431) TGGTGGGGTTAAAGACCGAAC 1 ThpsCp113 ( 80) TGGCGTTGGAGTAGGGAAAGC 1 ThpsCp105 ( 8) TGCTACGGTAAAACCGGGAAC 1 ThpsCp104 ( 381) TGCTACGGTAAAACCGGGAAC 1 ThpsCp115 ( 91) TAGGCCTGGATTAGCTACAAC 1 ThpsCp114 ( 212) TAGGCCTGGATTAGCTACAAC 1 ThpsCp097 ( 150) TGGTGGTGTAATATTTGGTCC 1 ThpsCp096 ( 283) TGGTATGGGAACAAGCCCAGG 1 ThpsCp124 ( 27) TGGTGTTGGGGATACTCAAAC 1 ThpsCp106 ( 288) TGTGGTTGTAAAAGTTGAAAG 1 ThpsCp093 ( 187) TGGGGTGGCAGGATTCGAACC 1 ThpsCp103 ( 251) TTGTAGTTCAACAGTTGGAAG 1 ThpsCp109 ( 159) TCGTGGTTTATCTGTTAGAAG 1 ThpsCp112 ( 421) TGGTCGTATAAAAGCTTTAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 9.77651 E= 4.2e-011 -1081 -1081 -1081 167 -179 -129 224 -250 -1081 -29 234 -250 -1081 -129 102 96 -79 29 189 -1081 -1081 71 160 -18 -1081 -1081 76 120 -279 -1081 213 -50 -1081 -29 124 67 101 -1081 -156 -92 53 -1081 76 -92 21 103 -156 -50 121 -1081 -1081 -150 -179 -29 202 -150 -279 129 102 -18 -1081 103 2 82 -21 103 102 -250 -21 29 143 -250 129 -1081 -1081 -250 91 -29 2 -1081 -1081 251 43 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 4.2e-011 0.000000 0.000000 0.000000 1.000000 0.111111 0.055556 0.777778 0.055556 0.000000 0.111111 0.833333 0.055556 0.000000 0.055556 0.333333 0.611111 0.222222 0.166667 0.611111 0.000000 0.000000 0.222222 0.500000 0.277778 0.000000 0.000000 0.277778 0.722222 0.055556 0.000000 0.722222 0.222222 0.000000 0.111111 0.388889 0.500000 0.777778 0.000000 0.055556 0.166667 0.555556 0.000000 0.277778 0.166667 0.444444 0.277778 0.055556 0.222222 0.888889 0.000000 0.000000 0.111111 0.111111 0.111111 0.666667 0.111111 0.055556 0.333333 0.333333 0.277778 0.000000 0.277778 0.166667 0.555556 0.333333 0.277778 0.333333 0.055556 0.333333 0.166667 0.444444 0.055556 0.944444 0.000000 0.000000 0.055556 0.722222 0.111111 0.166667 0.000000 0.000000 0.777778 0.222222 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TGG[TG][GA][GTC][TG][GT][TG]A[AG][ACT]AG[CGT][TC][AGC][GA]AA[CG] -------------------------------------------------------------------------------- Time 13.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 18 llr = 238 E-value = 6.3e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 6761a813344:34:1::23: pos.-specific C :139:12:213621:5:21:1 probability G 4::::16:32:36:a2152:9 matrix T 1211::272331:4:29357: bits 2.9 2.6 * 2.3 * 2.0 * * * Relative 1.7 * * * Entropy 1.4 ** * * * (19.1 bits) 1.2 ** * * * * 0.9 ** ** ** **** * 0.6 ******** ** **** ** 0.3 ********* *********** 0.0 --------------------- Multilevel AAACAAGTGAACGAGCTGTTG consensus GTC TAATCGAT G TGA sequence TGT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCp108 79 2.43e-09 AGAACATCAA AAACAATTCGCCGTGCTGATG GAATGTACAT ThpsCp107 345 2.43e-09 AGAACATCAA AAACAATTCGCCGTGCTGATG GAATGTACAT ThpsCp124 449 2.79e-08 GAAGGCGGCC GAACAATTGGTGCTGGTGTTG TTTCTAAAAT ThpsCp104 350 2.79e-08 TCACGTATGG GATCAGGTAAAGGTGCTGTTG ACTATTGGGT ThpsCp102 409 4.05e-08 AAACGTATTC GACCACGTGCCCAAGGTCGAG CTTATAAGAT ThpsCp100 8 1.39e-07 GGTAAAC GTCCAACTGTTCGAGGTTCAG TAATGAACCC ThpsCp099 285 1.39e-07 TTAGGTAAAC GTCCAACTGTTCGAGGTTCAG TAATGAACCC ThpsCp115 122 1.70e-07 ATTTTATTTA AAACAAGTAATGAAGCGGGTG ACCTTTTTTG ThpsCp114 243 1.70e-07 ATTTTATTTA AAACAAGTAATGAAGCGGGTG ACCTTTTTTG ThpsCp113 31 1.70e-07 GGTGGGAAAA AATTAAGTTTCCGTGCTGTTG TTGTTATAGG ThpsCp120 121 2.30e-07 ATTGGGATTG GAAAAAGAAAACGTGCTGTTG CAAGAGTATT ThpsCp103 464 7.41e-07 AAAGAAGCAA ACACAATTTACGGTGTTCTTG GTGTTAAAGT ThpsCp110 346 9.48e-07 CGCGTTAGTA AACCAGGATTACGAGTTTATG CTAATTCGAA ThpsCp101 226 1.11e-06 TTAAAATCTA ATCCAAGTGAACGCGATTTTC TTTTACAAGC ThpsCp097 50 1.30e-06 GTTTCAACAA AAACAAGAAGCGAAGTTCGAG GTGGTGGTAA ThpsCp116 227 2.18e-06 ACAGATGATA TTACAACAGAACAAGCTGTAG TATTAAGAAA ThpsCp122 172 4.59e-06 ATTACGAAAA AAACAAAATCACCCGCTTTAG TAAATTGTCC ThpsCp112 189 5.20e-06 ACAGTAGAAC GACCACGTCTATCTGTTTTTC GTTCTAATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp108 2.4e-09 78_[+3]_401 ThpsCp107 2.4e-09 344_[+3]_135 ThpsCp124 2.8e-08 448_[+3]_31 ThpsCp104 2.8e-08 349_[+3]_130 ThpsCp102 4e-08 408_[+3]_71 ThpsCp100 1.4e-07 7_[+3]_472 ThpsCp099 1.4e-07 284_[+3]_195 ThpsCp115 1.7e-07 121_[+3]_358 ThpsCp114 1.7e-07 242_[+3]_237 ThpsCp113 1.7e-07 30_[+3]_449 ThpsCp120 2.3e-07 120_[+3]_359 ThpsCp103 7.4e-07 463_[+3]_16 ThpsCp110 9.5e-07 345_[+3]_134 ThpsCp101 1.1e-06 225_[+3]_254 ThpsCp097 1.3e-06 49_[+3]_430 ThpsCp116 2.2e-06 226_[+3]_253 ThpsCp122 4.6e-06 171_[+3]_308 ThpsCp112 5.2e-06 188_[+3]_291 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=18 ThpsCp108 ( 79) AAACAATTCGCCGTGCTGATG 1 ThpsCp107 ( 345) AAACAATTCGCCGTGCTGATG 1 ThpsCp124 ( 449) GAACAATTGGTGCTGGTGTTG 1 ThpsCp104 ( 350) GATCAGGTAAAGGTGCTGTTG 1 ThpsCp102 ( 409) GACCACGTGCCCAAGGTCGAG 1 ThpsCp100 ( 8) GTCCAACTGTTCGAGGTTCAG 1 ThpsCp099 ( 285) GTCCAACTGTTCGAGGTTCAG 1 ThpsCp115 ( 122) AAACAAGTAATGAAGCGGGTG 1 ThpsCp114 ( 243) AAACAAGTAATGAAGCGGGTG 1 ThpsCp113 ( 31) AATTAAGTTTCCGTGCTGTTG 1 ThpsCp120 ( 121) GAAAAAGAAAACGTGCTGTTG 1 ThpsCp103 ( 464) ACACAATTTACGGTGTTCTTG 1 ThpsCp110 ( 346) AACCAGGATTACGAGTTTATG 1 ThpsCp101 ( 226) ATCCAAGTGAACGCGATTTTC 1 ThpsCp097 ( 50) AAACAAGAAGCGAAGTTCGAG 1 ThpsCp116 ( 227) TTACAACAGAACAAGCTGTAG 1 ThpsCp122 ( 172) AAACAAAATCACCCGCTTTAG 1 ThpsCp112 ( 189) GACCACGTCTATCTGTTTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 9.77651 E= 6.3e-010 53 -1081 124 -250 91 -129 -1081 -50 53 129 -1081 -150 -279 271 -1081 -250 138 -1081 -1081 -1081 101 -29 -56 -1081 -279 29 176 -50 -47 -1081 -1081 120 -47 29 102 -50 1 -29 43 -18 1 129 -1081 -18 -1081 216 102 -250 -47 29 176 -1081 21 -29 -1081 50 -1081 -1081 260 -1081 -279 188 43 -50 -1081 -1081 -56 150 -1081 29 160 8 -121 -29 43 67 -21 -1081 -1081 108 -1081 -29 243 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 6.3e-010 0.555556 0.000000 0.388889 0.055556 0.722222 0.055556 0.000000 0.222222 0.555556 0.333333 0.000000 0.111111 0.055556 0.888889 0.000000 0.055556 1.000000 0.000000 0.000000 0.000000 0.777778 0.111111 0.111111 0.000000 0.055556 0.166667 0.555556 0.222222 0.277778 0.000000 0.000000 0.722222 0.277778 0.166667 0.333333 0.222222 0.388889 0.111111 0.222222 0.277778 0.388889 0.333333 0.000000 0.277778 0.000000 0.611111 0.333333 0.055556 0.277778 0.166667 0.555556 0.000000 0.444444 0.111111 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 0.055556 0.500000 0.222222 0.222222 0.000000 0.000000 0.111111 0.888889 0.000000 0.166667 0.500000 0.333333 0.166667 0.111111 0.222222 0.500000 0.333333 0.000000 0.000000 0.666667 0.000000 0.111111 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][AT][AC]CAA[GT][TA][GAT][ATG][ACT][CG][GA][AT]G[CGT]T[GT][TG][TA]G -------------------------------------------------------------------------------- Time 20.64 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp093 4.96e-03 186_[+2(9.03e-07)]_293 ThpsCp095 2.83e-04 191_[+1(1.12e-07)]_288 ThpsCp096 1.54e-05 282_[+2(6.54e-07)]_115_\ [+1(7.79e-07)]_61 ThpsCp097 2.04e-11 49_[+3(1.30e-06)]_29_[+1(6.52e-10)]_\ 29_[+2(4.29e-07)]_330 ThpsCp098 4.15e-02 378_[+1(4.61e-06)]_101 ThpsCp099 2.83e-13 91_[+1(1.01e-07)]_172_\ [+3(1.39e-07)]_25_[+2(2.76e-10)]_1_[+1(8.46e-07)]_66_[+1(2.82e-05)]_40 ThpsCp100 2.11e-12 7_[+3(1.39e-07)]_25_[+2(2.76e-10)]_\ 1_[+1(8.46e-07)]_66_[+1(2.82e-05)]_209_[+1(7.11e-05)]_87 ThpsCp101 9.56e-03 225_[+3(1.11e-06)]_254 ThpsCp102 1.61e-04 408_[+3(4.05e-08)]_71 ThpsCp103 1.33e-08 250_[+2(2.58e-06)]_8_[+1(2.03e-07)]_\ 163_[+3(7.41e-07)]_16 ThpsCp104 2.81e-13 349_[+3(2.79e-08)]_10_\ [+2(2.10e-07)]_31_[+1(6.52e-10)]_47 ThpsCp105 6.43e-09 7_[+2(2.10e-07)]_31_[+1(6.52e-10)]_\ 420 ThpsCp106 1.73e-05 287_[+2(7.69e-07)]_139_\ [+1(2.31e-06)]_32 ThpsCp107 1.22e-11 94_[+1(2.31e-06)]_229_\ [+3(2.43e-09)]_80_[+1(7.74e-10)]_34 ThpsCp108 1.22e-11 78_[+3(2.43e-09)]_80_[+1(7.74e-10)]_\ 91_[+3(9.60e-05)]_188 ThpsCp109 4.07e-03 158_[+2(3.40e-06)]_321 ThpsCp110 3.42e-06 345_[+3(9.48e-07)]_98_\ [+1(1.67e-07)]_15 ThpsCp111 1.92e-04 67_[+2(3.54e-05)]_109_\ [+1(1.08e-06)]_282 ThpsCp112 4.94e-08 188_[+3(5.20e-06)]_211_\ [+2(4.74e-06)]_1_[+1(6.58e-08)]_37 ThpsCp113 1.77e-11 30_[+3(1.70e-07)]_28_[+2(1.08e-07)]_\ 162_[+2(3.10e-08)]_69_[+2(9.49e-05)]_127 ThpsCp114 2.62e-10 211_[+2(3.61e-07)]_10_\ [+3(1.70e-07)]_117_[+1(9.07e-08)]_99 ThpsCp115 2.62e-10 90_[+2(3.61e-07)]_10_[+3(1.70e-07)]_\ 117_[+1(9.07e-08)]_220 ThpsCp116 3.35e-03 226_[+3(2.18e-06)]_253 ThpsCp117 3.52e-04 202_[+2(5.81e-05)]_106_\ [+1(1.17e-06)]_150 ThpsCp118 5.81e-01 500 ThpsCp119 4.64e-03 152_[+1(4.61e-06)]_327 ThpsCp120 1.59e-12 120_[+3(2.30e-07)]_160_\ [+2(8.46e-10)]_16_[+1(1.24e-07)]_141 ThpsCp121 4.01e-09 33_[+2(8.46e-10)]_16_[+1(1.24e-07)]_\ 186_[+2(9.97e-06)]_202 ThpsCp122 9.12e-09 134_[+1(6.30e-05)]_16_\ [+3(4.59e-06)]_165_[+3(9.27e-05)]_[+3(9.94e-05)]_5_[+1(4.03e-06)]_5_\ [+2(1.40e-08)]_49 ThpsCp124 6.25e-10 26_[+2(7.09e-07)]_187_\ [+1(7.17e-07)]_193_[+3(2.79e-08)]_31 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************