******************************************************************************** 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/143/143.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 8976 1.0000 500 42712 1.0000 500 9320 1.0000 500 32326 1.0000 500 13160 1.0000 500 13382 1.0000 500 46897 1.0000 500 51026 1.0000 500 21430 1.0000 500 769 1.0000 500 38196 1.0000 500 47905 1.0000 500 52316 1.0000 500 29217 1.0000 500 32531 1.0000 500 18087 1.0000 500 6277 1.0000 500 39528 1.0000 500 42289 1.0000 500 30446 1.0000 500 51280 1.0000 500 25743 1.0000 500 41601 1.0000 500 44374 1.0000 500 33885 1.0000 500 10666 1.0000 500 44459 1.0000 500 26176 1.0000 500 8269 1.0000 500 27166 1.0000 500 45809 1.0000 500 12737 1.0000 500 50340 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/143/143.seqs.fa -oc motifs/143 -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= 33 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= 16500 N= 33 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.259 G 0.231 T 0.251 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.259 G 0.231 T 0.251 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 27 llr = 294 E-value = 1.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4663543333946434a8146 pos.-specific C 1:43:3:47:1613:2::3:2 probability G 54:4426316::3364:1551 matrix T ::::111::1:::::::1:1: bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * * Entropy 1.1 ** ** (15.7 bits) 0.8 ** * ** * ** 0.6 *** * * ***** * ***** 0.4 ***** *************** 0.2 ********************* 0.0 --------------------- Multilevel GAAGAAGCCGACAAGAAAGGA consensus AGCAGCAAAA AGGAG CAC sequence C G G C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 769 153 4.04e-08 TTCTCGGAAG CGAAAAGCCGACGAGGAAGAA TACGACAAGC 21430 258 4.84e-08 TTTGCGGGGA CGACGAACCGACAGGGAAGGA CCCGAACGAA 10666 408 9.54e-08 TATTGAACGA AAAGGAGCAAAAAAGCAAGGA AAAACGAAGG 32326 434 9.54e-08 AAGTTCGATT GGAAGAAGCGACACGCAAGGC CAAACAACAC 46897 217 5.32e-07 TGAATTGATC GAAGATGACGACAGGAAAGTC TTTTTCTGGC 30446 243 6.04e-07 GAGAGGGGGA GGACAGACAGAAGGGGAAGAA TTTGGCTTTG 52316 2 8.69e-07 A AAAAAAGCCAAAAGAGAACAG TGGAACGCTT 44374 172 1.10e-06 TCACGCCTGT GAAAACTGCGACGAAAAAGGC CGTCGTCACA 13160 324 1.37e-06 CGCAACCCCC GGAGACGCCACCAAAAAACAA GGTGCTTACG 51280 461 1.71e-06 ATACAACAAC AACAACAACAACACACAACAA GACAGTCTTT 8269 81 1.90e-06 TCCTGCGGAC AATGGCGCCGACGCGGAAGGC ATCAAGCTCT 39528 349 2.11e-06 AAGCAGGTGA GGCAAAGACGAACGGAATGGA CAAGGACGAC 33885 142 2.86e-06 CAACAGATTC GACCGCGACGACAAACAAAAC ACAGGATTGT 42712 158 2.86e-06 ATTCCTGATG AAAGAAAAAGACAGAAAGCGA ATGTCTCGAT 18087 63 3.47e-06 CATATTACCT AGCGGTGCGGACACGGAACAA GAGTACCGTT 38196 84 3.47e-06 TTCTTTGTCG GGAATGGCCAAAACGGAAGTC GCATCTCTGA 51026 69 3.81e-06 CGTACGGGAG AGCGAGAGAAAAACGGAAAGA AATGTGGCCC 6277 163 4.19e-06 CCGTGACCAT GACGAAGACTACGAGAATGTA CAGACGAACA 13382 243 6.56e-06 ATGCGTCCGA AGCCACGAAAACGAAGAAGGG CTTCTCAACG 27166 126 1.08e-05 TGACAGCCAA GCACGAGGCGACAGGAATCGG CGAGGTATAA 50340 424 1.36e-05 GGATACCGTG CGACGAACAAAAACACAACAA AGTTACACTT 25743 29 1.58e-05 TTTTGCCATG GAAGTCAGCTAACGGCAACGA CGAAAAGTGA 29217 251 1.58e-05 AGCGGGTCCG GACGGGTGCGACACCAATGGA CGGACCGGAC 47905 291 1.58e-05 AGAGAGGACA AACATGGACGAATGAAAACGA TGAAACTTAC 26176 376 2.10e-05 GTTTCGAGTA CAACGCAGCACCAAGGAAAAA CGGACGTACA 9320 243 4.26e-05 TTCCGGCGGT GAAGAAGGGGGCGAGAAAAAG GATTCCTACT 8976 113 8.23e-05 ATATAAAATA AACATGTCATAAAAGAAGGAA TCCTCCTCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 769 4e-08 152_[+1]_327 21430 4.8e-08 257_[+1]_222 10666 9.5e-08 407_[+1]_72 32326 9.5e-08 433_[+1]_46 46897 5.3e-07 216_[+1]_263 30446 6e-07 242_[+1]_237 52316 8.7e-07 1_[+1]_478 44374 1.1e-06 171_[+1]_308 13160 1.4e-06 323_[+1]_156 51280 1.7e-06 460_[+1]_19 8269 1.9e-06 80_[+1]_399 39528 2.1e-06 348_[+1]_131 33885 2.9e-06 141_[+1]_338 42712 2.9e-06 157_[+1]_322 18087 3.5e-06 62_[+1]_417 38196 3.5e-06 83_[+1]_396 51026 3.8e-06 68_[+1]_411 6277 4.2e-06 162_[+1]_317 13382 6.6e-06 242_[+1]_237 27166 1.1e-05 125_[+1]_354 50340 1.4e-05 423_[+1]_56 25743 1.6e-05 28_[+1]_451 29217 1.6e-05 250_[+1]_229 47905 1.6e-05 290_[+1]_189 26176 2.1e-05 375_[+1]_104 9320 4.3e-05 242_[+1]_237 8976 8.2e-05 112_[+1]_367 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=27 769 ( 153) CGAAAAGCCGACGAGGAAGAA 1 21430 ( 258) CGACGAACCGACAGGGAAGGA 1 10666 ( 408) AAAGGAGCAAAAAAGCAAGGA 1 32326 ( 434) GGAAGAAGCGACACGCAAGGC 1 46897 ( 217) GAAGATGACGACAGGAAAGTC 1 30446 ( 243) GGACAGACAGAAGGGGAAGAA 1 52316 ( 2) AAAAAAGCCAAAAGAGAACAG 1 44374 ( 172) GAAAACTGCGACGAAAAAGGC 1 13160 ( 324) GGAGACGCCACCAAAAAACAA 1 51280 ( 461) AACAACAACAACACACAACAA 1 8269 ( 81) AATGGCGCCGACGCGGAAGGC 1 39528 ( 349) GGCAAAGACGAACGGAATGGA 1 33885 ( 142) GACCGCGACGACAAACAAAAC 1 42712 ( 158) AAAGAAAAAGACAGAAAGCGA 1 18087 ( 63) AGCGGTGCGGACACGGAACAA 1 38196 ( 84) GGAATGGCCAAAACGGAAGTC 1 51026 ( 69) AGCGAGAGAAAAACGGAAAGA 1 6277 ( 163) GACGAAGACTACGAGAATGTA 1 13382 ( 243) AGCCACGAAAACGAAGAAGGG 1 27166 ( 126) GCACGAGGCGACAGGAATCGG 1 50340 ( 424) CGACGAACAAAAACACAACAA 1 25743 ( 29) GAAGTCAGCTAACGGCAACGA 1 29217 ( 251) GACGGGTGCGACACCAATGGA 1 47905 ( 291) AACATGGACGAATGAAAACGA 1 26176 ( 376) CAACGCAGCACCAAGGAAAAA 1 9320 ( 243) GAAGAAGGGGGCGAGAAAAAG 1 8976 ( 113) AACATGTCATAAAAGAAGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15840 bayes= 10.3895 E= 1.8e-004 52 -81 106 -1140 110 -280 82 -1140 120 52 -1140 -276 37 0 82 -1140 90 -1140 68 -76 65 19 -6 -176 37 -1140 127 -118 20 65 36 -1140 0 136 -164 -1140 37 -1140 127 -118 178 -181 -264 -1140 52 128 -1140 -1140 128 -181 17 -276 52 19 53 -1140 37 -280 145 -1140 65 -22 68 -1140 195 -1140 -1140 -1140 159 -1140 -164 -76 -80 36 117 -1140 65 -1140 106 -118 128 -22 -64 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 1.8e-004 0.370370 0.148148 0.481481 0.000000 0.555556 0.037037 0.407407 0.000000 0.592593 0.370370 0.000000 0.037037 0.333333 0.259259 0.407407 0.000000 0.481481 0.000000 0.370370 0.148148 0.407407 0.296296 0.222222 0.074074 0.333333 0.000000 0.555556 0.111111 0.296296 0.407407 0.296296 0.000000 0.259259 0.666667 0.074074 0.000000 0.333333 0.000000 0.555556 0.111111 0.888889 0.074074 0.037037 0.000000 0.370370 0.629630 0.000000 0.000000 0.629630 0.074074 0.259259 0.037037 0.370370 0.296296 0.333333 0.000000 0.333333 0.037037 0.629630 0.000000 0.407407 0.222222 0.370370 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.074074 0.148148 0.148148 0.333333 0.518519 0.000000 0.407407 0.000000 0.481481 0.111111 0.629630 0.222222 0.148148 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA][AG][AC][GAC][AG][ACG][GA][CAG][CA][GA]A[CA][AG][AGC][GA][AGC]AA[GC][GA][AC] -------------------------------------------------------------------------------- Time 11.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 15 llr = 175 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 72:17:7:::85221 pos.-specific C :3:63a1::9::531 probability G 3:13:::a:122:37 matrix T :59:::3:a::331: bits 2.1 * 1.9 * ** 1.7 * * *** 1.5 * * *** Relative 1.3 * * **** Entropy 1.1 * * ** **** * (16.9 bits) 0.8 * ********* * 0.6 * ********* * 0.4 ************* * 0.2 ************* * 0.0 --------------- Multilevel ATTCACAGTCAACCG consensus GC GC T GTTG sequence A GAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 26176 352 8.84e-08 AAGGTTTCGC ACTCACAGTCAACTG TTTCGAGTAC 27166 200 1.74e-07 ACAAATAATA ATTCACAGTCAAAAG CTTTTACTGT 29217 144 1.74e-07 CCACCCACCC AATCACAGTCAATCG TCGACGCACC 45809 319 2.71e-07 AAAAGCGTTC ATTCACTGTCATTCG TTCATTAGTT 32531 162 4.11e-07 GTGGATTCAC ATTCACTGTCAGCAG GACTACATTT 33885 281 1.03e-06 TTGTTTGGGC AATCACAGTCATCGA TTTCCCCCAC 41601 347 2.42e-06 CGTGTCATTC GTTCCCAGTCGAAGG AAAAGCAACA 46897 405 2.64e-06 GGCCCGTCGT ATTACCAGTCAACAG GAAACGTCGT 8269 146 3.11e-06 CGTGCGATCT GCGGACAGTCAACCG GGCATGGTCT 44459 183 3.11e-06 GGAAACCAGC ACTGACAGTGAGCGG GATTCACTCT 25743 104 3.96e-06 CCGAAAACGT GCTCACAGTCAGTCA TACACCATAC 8976 147 4.60e-06 TCCTCCTAGA GATGCCAGTCGTCCG AATTCGCGTA 12737 137 6.51e-06 TAATGTCACT GTTGCCTGTCATCGC CAGGACGCAC 51280 132 6.94e-06 TGACCGACTG ACTGACCGTCGATGG GACAACAACG 47905 168 7.42e-06 TTGAAGCCTT ATTCACTGTCATATC AGGCTGGTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 26176 8.8e-08 351_[+2]_134 27166 1.7e-07 199_[+2]_286 29217 1.7e-07 143_[+2]_342 45809 2.7e-07 318_[+2]_167 32531 4.1e-07 161_[+2]_324 33885 1e-06 280_[+2]_205 41601 2.4e-06 346_[+2]_139 46897 2.6e-06 404_[+2]_81 8269 3.1e-06 145_[+2]_340 44459 3.1e-06 182_[+2]_303 25743 4e-06 103_[+2]_382 8976 4.6e-06 146_[+2]_339 12737 6.5e-06 136_[+2]_349 51280 6.9e-06 131_[+2]_354 47905 7.4e-06 167_[+2]_318 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=15 26176 ( 352) ACTCACAGTCAACTG 1 27166 ( 200) ATTCACAGTCAAAAG 1 29217 ( 144) AATCACAGTCAATCG 1 45809 ( 319) ATTCACTGTCATTCG 1 32531 ( 162) ATTCACTGTCAGCAG 1 33885 ( 281) AATCACAGTCATCGA 1 41601 ( 347) GTTCCCAGTCGAAGG 1 46897 ( 405) ATTACCAGTCAACAG 1 8269 ( 146) GCGGACAGTCAACCG 1 44459 ( 183) ACTGACAGTGAGCGG 1 25743 ( 104) GCTCACAGTCAGTCA 1 8976 ( 147) GATGCCAGTCGTCCG 1 12737 ( 137) GTTGCCTGTCATCGC 1 51280 ( 132) ACTGACCGTCGATGG 1 47905 ( 168) ATTCACTGTCATATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 16038 bayes= 10.7357 E= 1.1e+000 136 -1055 53 -1055 -37 36 -1055 89 -1055 -1055 -179 189 -195 121 53 -1055 150 4 -1055 -1055 -1055 195 -1055 -1055 136 -196 -1055 9 -1055 -1055 211 -1055 -1055 -1055 -1055 199 -1055 185 -179 -1055 163 -1055 -21 -1055 85 -1055 -21 41 -37 104 -1055 9 -37 36 53 -91 -96 -96 167 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 15 E= 1.1e+000 0.666667 0.000000 0.333333 0.000000 0.200000 0.333333 0.000000 0.466667 0.000000 0.000000 0.066667 0.933333 0.066667 0.600000 0.333333 0.000000 0.733333 0.266667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.066667 0.000000 0.266667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.933333 0.066667 0.000000 0.800000 0.000000 0.200000 0.000000 0.466667 0.000000 0.200000 0.333333 0.200000 0.533333 0.000000 0.266667 0.200000 0.333333 0.333333 0.133333 0.133333 0.133333 0.733333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][TCA]T[CG][AC]C[AT]GTC[AG][ATG][CTA][CGA]G -------------------------------------------------------------------------------- Time 22.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 27 llr = 260 E-value = 2.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1::::12::2::1:2 pos.-specific C :8:3163163121:42 probability G 11:1116:::::64:1 matrix T 8:a673:747783565 bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 * * * Entropy 1.1 * * * * (13.9 bits) 0.8 **** *** ** * 0.6 *************** 0.4 *************** 0.2 **************** 0.0 ---------------- Multilevel TCTTTCGTCTTTGTTT consensus C TCATC CTGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 18087 122 1.08e-07 TGGGACACAC TCTCTCCTCTTTGGTA CACACGGTAC 41601 280 2.34e-07 ATCGGACGGC TCTTTCGTCTTTCTTC TTGCCCAACC 52316 196 4.17e-07 GATGAAGAGT TCTCTCGTCCTTGTTG CTGTTGTGCT 46897 86 9.31e-07 AAGCCCATGG TGTTTTGTTTTCGGTT TTGATTTCGA 13160 112 9.31e-07 GATAACCTCC TCTTTTCTCCCTGGTT CCGTCTCATT 9320 460 1.53e-06 ACATCGTCGC TCTTTCCTTTATTGTC GCGGATGTTC 29217 408 2.18e-06 CATTTGCCAA TCTTTCCACCTTGTCA CAGTCCTACC 39528 230 2.74e-06 CGGTGTGGAG TATTTTGTTTCTGTTT ACATCACTTC 26176 192 4.73e-06 ATGAATTTCC TCTTTCGTTTCCGATT CTAATCTCGA 44374 357 4.73e-06 TATTCAACAG TGTCTTGCTTTTGTTT TGGGACGACC 51026 369 7.90e-06 CAATCCACCG TCGTTTGTCTTTGTCG CTCAACAGAC 50340 93 1.40e-05 GTCGCTGCAC TCTCGGGACTTTGGCT CCGGTCACAA 30446 406 1.40e-05 CACAAACGGA TCTCTTCTTTCTCTCT CATTGTACAC 8976 410 1.68e-05 TGCGTATACT TCTCACCCCTTTGTTT TCTTGGACTG 38196 304 2.01e-05 TAATCTATAA TCTCCCGACTTTGATC CGTGATTCAT 21430 399 2.01e-05 GTTAGATTCT TCTTCCACTTTTGTCT AGATTTCGTA 13382 401 2.20e-05 CTTCTATTCT TCTGGCGTCTTCTGCT CACGCCTTTA 12737 434 2.84e-05 TAAACATCAT GCTTTCGTCCATCTTC TCCAAATCGA 10666 110 3.08e-05 AGAGCCACTC GTTTTTGATTTTGTCT CCCCAACCAA 42712 316 3.08e-05 GCATATACTT TGTTTCATCCTTTGTA AATCTAACAA 32531 331 3.94e-05 GAATCCGAGG GCTCGCGTTGTTGGTT TACGGTGCCT 45809 370 4.62e-05 CAACTTTGTT TCTTCTCTCCACTGTT GCGATCTGAA 8269 200 4.62e-05 ACTATTGGAA ACTTTCGTTCATGTCA GCTACGGATG 44459 33 4.62e-05 CTCAAGGAGC TCTTTCTATTATTTTC AAGCCAAAGA 6277 25 4.62e-05 CTAGCGGCGA TCTTTGCTGTTCTGTT GGCAAATCGC 27166 319 5.39e-05 GCCCAGAACC TATTCTCTCTTTTGCA AAGGAACAAG 32326 68 7.27e-05 CCGTGCGGGT GCTGTCGACTTCGGCG TCGAACGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 18087 1.1e-07 121_[+3]_363 41601 2.3e-07 279_[+3]_205 52316 4.2e-07 195_[+3]_289 46897 9.3e-07 85_[+3]_399 13160 9.3e-07 111_[+3]_373 9320 1.5e-06 459_[+3]_25 29217 2.2e-06 407_[+3]_77 39528 2.7e-06 229_[+3]_255 26176 4.7e-06 191_[+3]_293 44374 4.7e-06 356_[+3]_128 51026 7.9e-06 368_[+3]_116 50340 1.4e-05 92_[+3]_392 30446 1.4e-05 405_[+3]_79 8976 1.7e-05 409_[+3]_75 38196 2e-05 303_[+3]_181 21430 2e-05 398_[+3]_86 13382 2.2e-05 400_[+3]_84 12737 2.8e-05 433_[+3]_51 10666 3.1e-05 109_[+3]_375 42712 3.1e-05 315_[+3]_169 32531 3.9e-05 330_[+3]_154 45809 4.6e-05 369_[+3]_115 8269 4.6e-05 199_[+3]_285 44459 4.6e-05 32_[+3]_452 6277 4.6e-05 24_[+3]_460 27166 5.4e-05 318_[+3]_166 32326 7.3e-05 67_[+3]_417 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=27 18087 ( 122) TCTCTCCTCTTTGGTA 1 41601 ( 280) TCTTTCGTCTTTCTTC 1 52316 ( 196) TCTCTCGTCCTTGTTG 1 46897 ( 86) TGTTTTGTTTTCGGTT 1 13160 ( 112) TCTTTTCTCCCTGGTT 1 9320 ( 460) TCTTTCCTTTATTGTC 1 29217 ( 408) TCTTTCCACCTTGTCA 1 39528 ( 230) TATTTTGTTTCTGTTT 1 26176 ( 192) TCTTTCGTTTCCGATT 1 44374 ( 357) TGTCTTGCTTTTGTTT 1 51026 ( 369) TCGTTTGTCTTTGTCG 1 50340 ( 93) TCTCGGGACTTTGGCT 1 30446 ( 406) TCTCTTCTTTCTCTCT 1 8976 ( 410) TCTCACCCCTTTGTTT 1 38196 ( 304) TCTCCCGACTTTGATC 1 21430 ( 399) TCTTCCACTTTTGTCT 1 13382 ( 401) TCTGGCGTCTTCTGCT 1 12737 ( 434) GCTTTCGTCCATCTTC 1 10666 ( 110) GTTTTTGATTTTGTCT 1 42712 ( 316) TGTTTCATCCTTTGTA 1 32531 ( 331) GCTCGCGTTGTTGGTT 1 45809 ( 370) TCTTCTCTCCACTGTT 1 8269 ( 200) ACTTTCGTTCATGTCA 1 44459 ( 33) TCTTTCTATTATTTTC 1 6277 ( 25) TCTTTGCTGTTCTGTT 1 27166 ( 319) TATTCTCTCTTTTGCA 1 32326 ( 68) GCTGTCGACTTCGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16005 bayes= 9.77873 E= 2.1e+000 -280 -1140 -64 170 -180 159 -106 -276 -1140 -1140 -264 194 -1140 19 -164 133 -280 -81 -106 149 -1140 119 -164 41 -180 36 127 -276 -22 -122 -1140 141 -1140 110 -264 70 -1140 0 -264 149 -48 -81 -1140 141 -1140 -22 -1140 163 -1140 -122 145 5 -180 -1140 94 94 -1140 52 -1140 133 -48 -48 -106 105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 27 E= 2.1e+000 0.037037 0.000000 0.148148 0.814815 0.074074 0.777778 0.111111 0.037037 0.000000 0.000000 0.037037 0.962963 0.000000 0.296296 0.074074 0.629630 0.037037 0.148148 0.111111 0.703704 0.000000 0.592593 0.074074 0.333333 0.074074 0.333333 0.555556 0.037037 0.222222 0.111111 0.000000 0.666667 0.000000 0.555556 0.037037 0.407407 0.000000 0.259259 0.037037 0.703704 0.185185 0.148148 0.000000 0.666667 0.000000 0.222222 0.000000 0.777778 0.000000 0.111111 0.629630 0.259259 0.074074 0.000000 0.444444 0.481481 0.000000 0.370370 0.000000 0.629630 0.185185 0.185185 0.111111 0.518519 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TCT[TC]T[CT][GC][TA][CT][TC]T[TC][GT][TG][TC]T -------------------------------------------------------------------------------- Time 33.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8976 8.12e-05 112_[+1(8.23e-05)]_13_\ [+2(4.60e-06)]_248_[+3(1.68e-05)]_75 42712 2.54e-04 157_[+1(2.86e-06)]_137_\ [+3(3.08e-05)]_169 9320 4.95e-04 242_[+1(4.26e-05)]_196_\ [+3(1.53e-06)]_25 32326 1.00e-04 67_[+3(7.27e-05)]_350_\ [+1(9.54e-08)]_46 13160 2.98e-05 111_[+3(9.31e-07)]_196_\ [+1(1.37e-06)]_156 13382 1.23e-03 242_[+1(6.56e-06)]_137_\ [+3(2.20e-05)]_84 46897 4.14e-08 85_[+3(9.31e-07)]_115_\ [+1(5.32e-07)]_167_[+2(2.64e-06)]_81 51026 1.01e-04 68_[+1(3.81e-06)]_279_\ [+3(7.90e-06)]_116 21430 1.57e-05 257_[+1(4.84e-08)]_120_\ [+3(2.01e-05)]_38_[+3(9.67e-05)]_32 769 6.50e-04 152_[+1(4.04e-08)]_170_\ [+1(4.19e-06)]_136 38196 1.96e-04 83_[+1(3.47e-06)]_199_\ [+3(2.01e-05)]_181 47905 6.72e-04 167_[+2(7.42e-06)]_108_\ [+1(1.58e-05)]_189 52316 7.00e-07 1_[+1(8.69e-07)]_173_[+3(4.17e-07)]_\ 289 29217 1.65e-07 143_[+2(1.74e-07)]_92_\ [+1(1.58e-05)]_136_[+3(2.18e-06)]_77 32531 2.00e-04 161_[+2(4.11e-07)]_154_\ [+3(3.94e-05)]_154 18087 7.69e-06 62_[+1(3.47e-06)]_38_[+3(1.08e-07)]_\ 363 6277 5.88e-04 24_[+3(4.62e-05)]_122_\ [+1(4.19e-06)]_317 39528 1.14e-04 229_[+3(2.74e-06)]_103_\ [+1(2.11e-06)]_131 42289 7.84e-01 500 30446 5.21e-05 215_[+3(9.67e-05)]_11_\ [+1(6.04e-07)]_142_[+3(1.40e-05)]_79 51280 2.12e-04 67_[+1(5.37e-05)]_43_[+2(6.94e-06)]_\ 314_[+1(1.71e-06)]_19 25743 4.73e-04 28_[+1(1.58e-05)]_54_[+2(3.96e-06)]_\ 382 41601 1.08e-05 279_[+3(2.34e-07)]_51_\ [+2(2.42e-06)]_139 44374 1.22e-04 171_[+1(1.10e-06)]_164_\ [+3(4.73e-06)]_128 33885 6.33e-05 141_[+1(2.86e-06)]_118_\ [+2(1.03e-06)]_205 10666 2.26e-05 109_[+3(3.08e-05)]_282_\ [+1(9.54e-08)]_2_[+1(3.13e-05)]_49 44459 7.81e-04 32_[+3(4.62e-05)]_134_\ [+2(3.11e-06)]_303 26176 2.34e-07 191_[+3(4.73e-06)]_144_\ [+2(8.84e-08)]_9_[+1(2.10e-05)]_104 8269 5.12e-06 80_[+1(1.90e-06)]_44_[+2(3.11e-06)]_\ 39_[+3(4.62e-05)]_285 27166 2.10e-06 125_[+1(1.08e-05)]_53_\ [+2(1.74e-07)]_104_[+3(5.39e-05)]_166 45809 2.00e-04 318_[+2(2.71e-07)]_36_\ [+3(4.62e-05)]_115 12737 2.36e-03 136_[+2(6.51e-06)]_282_\ [+3(2.84e-05)]_51 50340 1.07e-03 92_[+3(1.40e-05)]_315_\ [+1(1.36e-05)]_56 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************