******************************************************************************** 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/431/431.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10027 1.0000 500 10479 1.0000 500 10523 1.0000 500 10976 1.0000 500 11127 1.0000 500 11454 1.0000 500 12021 1.0000 500 21033 1.0000 500 21339 1.0000 500 21819 1.0000 500 22776 1.0000 500 24132 1.0000 500 24464 1.0000 500 24491 1.0000 500 25262 1.0000 500 25505 1.0000 500 25808 1.0000 500 264533 1.0000 500 2646 1.0000 500 37564 1.0000 500 39913 1.0000 500 6426 1.0000 500 6534 1.0000 500 7153 1.0000 500 7311 1.0000 500 7313 1.0000 500 9911 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/431/431.seqs.fa -oc motifs/431 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.231 G 0.254 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.231 G 0.254 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 22 llr = 249 E-value = 3.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::23:1:::3:1::::111:: pos.-specific C 163184:16135:235262:a probability G 4:24:352:6::8::36::4: matrix T 543312564:7428731366: bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * * * Entropy 1.1 * * * * ** ** (16.3 bits) 0.8 * * * * * *** ** 0.6 ** * *** * *** **** 0.4 ** * *************** 0.2 ** ****************** 0.0 --------------------- Multilevel TCCGCCGTCGTCGTTCGCTTC consensus GTTA GTGTACTT CG TCG sequence AT T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7313 412 5.17e-10 CGTCCTCCAG TCAACGTTCGTTGTTCGCTGC TCCCATCATC 7311 412 5.17e-10 CGTCCTCCAG TCAACGTTCGTTGTTCGCTGC TCCCATCATC 12021 372 4.47e-08 AAAGATGATG TCTTCCTTTATTGTCCCCTTC TTATTTTCAC 24491 82 2.87e-07 GCCTAATTTT TCATCCGTTGCAGTTCGTTGC CGAAATATGA 22776 359 3.23e-07 TCTAAGCATA TCATCTTTCTTCGTCGGCTTC ATCTCCTCAA 11127 326 7.09e-07 GGCCATCGTC GCTGCGTTCGTGGCTGGCTGC GGTCGCGGAA 37564 453 9.72e-07 CGCTCGTCGT TCGTCCGTCGTCTTTCAACTC GCACCCACTC 10523 308 1.32e-06 GACCGGCTTG TCCCCTGGTGTCTTTTGTTTC GCAAAGGATT 10027 259 1.32e-06 CTGCCGCTTC GTCGTCGTCGTTGTCTGTCTC GCCAACCTAC 7153 281 1.45e-06 AGGTTCGGTT GTTGCTTGCATCTTTCTCTTC ACTCAAACAC 9911 17 1.76e-06 TCTCTCCATT GTTGCCGTTGCTGTTGGAATC GTCGTAGAGA 6534 58 2.12e-06 TGCCACTATT TTCTCCTTTACATTTTGCTTC TTCTTCAAGT 25505 475 2.55e-06 GCGGCGGAGG CTGGCAGGCGTTGTTCCCTGC GAATG 21339 410 3.33e-06 ATCGCTTCCT CTCACCTTCGCCGCCTCCTTC CACACTCGCT 11454 164 6.46e-06 TTGGGTGCGT GTTGCCGTCCTCGTCGTCAGC CGAGTGGAAG 2646 473 7.55e-06 CCACGTATCA TCAATAGTTGTCGTTGCTCTC CACGAAA 25808 240 1.02e-05 GCGACGGTGA GCTGCTGCCACTTTCGGCATC CCACGGAAGG 10976 292 1.02e-05 GTCAACCGTC TCGACGTTCGTCGTACGTCTG GTGGGAGAGA 24464 245 1.36e-05 GCCGAGGAGG GCCGCGGCTACTGCTTGATGC TTCGCCATGT 21033 381 2.03e-05 TGTATTCAGC TTGCTCTGCGTCGCTTTTTTC GCACCGTGGG 6426 283 2.17e-05 TCTCTTGACA GCCAATTCCATTGATCGCTTC TCACTCCCTC 39913 363 4.19e-05 CTCCTCCTCG TCGTCGGGTCACGTTCACCGC CATTGCGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7313 5.2e-10 411_[+1]_68 7311 5.2e-10 411_[+1]_68 12021 4.5e-08 371_[+1]_108 24491 2.9e-07 81_[+1]_398 22776 3.2e-07 358_[+1]_121 11127 7.1e-07 325_[+1]_154 37564 9.7e-07 452_[+1]_27 10523 1.3e-06 307_[+1]_172 10027 1.3e-06 258_[+1]_221 7153 1.5e-06 280_[+1]_199 9911 1.8e-06 16_[+1]_463 6534 2.1e-06 57_[+1]_422 25505 2.6e-06 474_[+1]_5 21339 3.3e-06 409_[+1]_70 11454 6.5e-06 163_[+1]_316 2646 7.6e-06 472_[+1]_7 25808 1e-05 239_[+1]_240 10976 1e-05 291_[+1]_188 24464 1.4e-05 244_[+1]_235 21033 2e-05 380_[+1]_99 6426 2.2e-05 282_[+1]_197 39913 4.2e-05 362_[+1]_117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=22 7313 ( 412) TCAACGTTCGTTGTTCGCTGC 1 7311 ( 412) TCAACGTTCGTTGTTCGCTGC 1 12021 ( 372) TCTTCCTTTATTGTCCCCTTC 1 24491 ( 82) TCATCCGTTGCAGTTCGTTGC 1 22776 ( 359) TCATCTTTCTTCGTCGGCTTC 1 11127 ( 326) GCTGCGTTCGTGGCTGGCTGC 1 37564 ( 453) TCGTCCGTCGTCTTTCAACTC 1 10523 ( 308) TCCCCTGGTGTCTTTTGTTTC 1 10027 ( 259) GTCGTCGTCGTTGTCTGTCTC 1 7153 ( 281) GTTGCTTGCATCTTTCTCTTC 1 9911 ( 17) GTTGCCGTTGCTGTTGGAATC 1 6534 ( 58) TTCTCCTTTACATTTTGCTTC 1 25505 ( 475) CTGGCAGGCGTTGTTCCCTGC 1 21339 ( 410) CTCACCTTCGCCGCCTCCTTC 1 11454 ( 164) GTTGCCGTCCTCGTCGTCAGC 1 2646 ( 473) TCAATAGTTGTCGTTGCTCTC 1 25808 ( 240) GCTGCTGCCACTTTCGGCATC 1 10976 ( 292) TCGACGTTCGTCGTACGTCTG 1 24464 ( 245) GCCGCGGCTACTGCTTGATGC 1 21033 ( 381) TTGCTCTGCGTCGCTTTTTTC 1 6426 ( 283) GCCAATTCCATTGATCGCTTC 1 39913 ( 363) TCGTCGGGTCACGTTCACCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 9.55553 E= 3.0e-003 -1110 -134 52 108 -1110 146 -1110 50 -18 24 -16 8 8 -134 52 8 -250 183 -1110 -92 -150 83 10 -18 -1110 -1110 98 96 -1110 -76 -16 131 -1110 146 -1110 50 8 -134 122 -250 -250 24 -1110 140 -150 98 -248 67 -1110 -1110 161 -18 -250 -34 -1110 159 -250 24 -1110 140 -1110 98 10 8 -150 -34 122 -92 -92 136 -1110 8 -92 -2 -1110 131 -1110 -1110 52 131 -1110 205 -248 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 3.0e-003 0.000000 0.090909 0.363636 0.545455 0.000000 0.636364 0.000000 0.363636 0.227273 0.272727 0.227273 0.272727 0.272727 0.090909 0.363636 0.272727 0.045455 0.818182 0.000000 0.136364 0.090909 0.409091 0.272727 0.227273 0.000000 0.000000 0.500000 0.500000 0.000000 0.136364 0.227273 0.636364 0.000000 0.636364 0.000000 0.363636 0.272727 0.090909 0.590909 0.045455 0.045455 0.272727 0.000000 0.681818 0.090909 0.454545 0.045455 0.409091 0.000000 0.000000 0.772727 0.227273 0.045455 0.181818 0.000000 0.772727 0.045455 0.272727 0.000000 0.681818 0.000000 0.454545 0.272727 0.272727 0.090909 0.181818 0.590909 0.136364 0.136364 0.590909 0.000000 0.272727 0.136364 0.227273 0.000000 0.636364 0.000000 0.000000 0.363636 0.636364 0.000000 0.954545 0.045455 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][CT][CTAG][GAT]C[CGT][GT][TG][CT][GA][TC][CT][GT]T[TC][CGT]G[CT][TC][TG]C -------------------------------------------------------------------------------- Time 5.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 22 llr = 209 E-value = 9.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1965376:a9:1 pos.-specific C 7133513a:1a6 probability G 2::::11::::: matrix T ::123::::::3 bits 2.1 * * 1.9 ** * 1.7 ** * 1.5 * **** Relative 1.3 * **** Entropy 1.1 * **** (13.7 bits) 0.8 *** ***** 0.6 *** ******* 0.4 *** ******** 0.2 ************ 0.0 ------------ Multilevel CAAACAACAACC consensus CCA C T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 6534 465 5.00e-08 CGCCCAGCAT CAAACAACAACC AAACAACACT 264533 489 9.49e-08 GTCTCTATCT CAACCAACAACC 25262 81 3.06e-06 CGAACAAACC CAAATCACAACC TCGCAGGTGA 37564 489 3.49e-06 CACTCCAACA CACTTAACAACC 10027 211 4.41e-06 CAACCAAGCT CCAAAAACAACC CCGTCAACGC 39913 484 4.95e-06 ATTGGTGCCG CAACACACAACC GGCGA 10976 213 6.60e-06 GCAGACAAAA CACACAGCAACC GTCGTTTGAT 10523 369 6.60e-06 ACATGTTTTA AAATCAACAACC AAGTCACAAG 9911 446 7.52e-06 ACGACGTGAG GACAAAACAACC GCAGATGTAC 7313 280 8.62e-06 CAAGCTAAGC AAACCAACAACT CGTTCATTCC 25505 249 8.62e-06 AACGCACCTA GAAAAAACAACT AGGCAAAGAA 21339 61 1.32e-05 CATGTATTGA CACTCAACAACA ACATAGAGAG 6426 202 1.94e-05 CGACGGCATG CATCTAACAACT ACGCTCTGAC 24491 18 2.09e-05 AGTATAATTG CAAGTAACAACT GTAGAAGTAA 7153 450 2.32e-05 GCTAGCGACT GACCTACCAACC AACCCCTCCC 24132 484 3.52e-05 CCACAGCGAA CATACACCAACA CGAAG 10479 479 4.16e-05 TTACACTCCC CAATCTCCAACC TCCAGGGCTC 25808 142 5.21e-05 TCTTACCTGA CCAACACCACCC GTACCACCAA 11127 11 7.45e-05 TTCTCTTTTC GAACTGACAACT GAAGTTGGGT 24464 451 8.57e-05 CGCCGAGGCA CAACACCCACCC TGTAGCAGCA 12021 147 1.21e-04 GGCACTCCTT CCAAAGCCAACT GCACCTGCAC 11454 88 1.28e-04 AGCACATACA AACACAGCAACA GAGGGAGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6534 5e-08 464_[+2]_24 264533 9.5e-08 488_[+2] 25262 3.1e-06 80_[+2]_408 37564 3.5e-06 488_[+2] 10027 4.4e-06 210_[+2]_278 39913 5e-06 483_[+2]_5 10976 6.6e-06 212_[+2]_276 10523 6.6e-06 368_[+2]_120 9911 7.5e-06 445_[+2]_43 7313 8.6e-06 279_[+2]_209 25505 8.6e-06 248_[+2]_240 21339 1.3e-05 60_[+2]_428 6426 1.9e-05 201_[+2]_287 24491 2.1e-05 17_[+2]_471 7153 2.3e-05 449_[+2]_39 24132 3.5e-05 483_[+2]_5 10479 4.2e-05 478_[+2]_10 25808 5.2e-05 141_[+2]_347 11127 7.4e-05 10_[+2]_478 24464 8.6e-05 450_[+2]_38 12021 0.00012 146_[+2]_342 11454 0.00013 87_[+2]_401 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=22 6534 ( 465) CAAACAACAACC 1 264533 ( 489) CAACCAACAACC 1 25262 ( 81) CAAATCACAACC 1 37564 ( 489) CACTTAACAACC 1 10027 ( 211) CCAAAAACAACC 1 39913 ( 484) CAACACACAACC 1 10976 ( 213) CACACAGCAACC 1 10523 ( 369) AAATCAACAACC 1 9911 ( 446) GACAAAACAACC 1 7313 ( 280) AAACCAACAACT 1 25505 ( 249) GAAAAAACAACT 1 21339 ( 61) CACTCAACAACA 1 6426 ( 202) CATCTAACAACT 1 24491 ( 18) CAAGTAACAACT 1 7153 ( 450) GACCTACCAACC 1 24132 ( 484) CATACACCAACA 1 10479 ( 479) CAATCTCCAACC 1 25808 ( 142) CCAACACCACCC 1 11127 ( 11) GAACTGACAACT 1 24464 ( 451) CAACACCCACCC 1 12021 ( 147) CCAAAGCCAACT 1 11454 ( 88) AACACAGCAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13203 bayes= 9.58236 E= 9.5e-004 -92 156 -48 -1110 174 -76 -1110 -1110 130 24 -1110 -150 82 46 -248 -50 8 98 -1110 8 149 -76 -148 -250 130 24 -148 -1110 -1110 212 -1110 -1110 195 -1110 -1110 -1110 182 -134 -1110 -1110 -1110 212 -1110 -1110 -92 136 -1110 8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 22 E= 9.5e-004 0.136364 0.681818 0.181818 0.000000 0.863636 0.136364 0.000000 0.000000 0.636364 0.272727 0.000000 0.090909 0.454545 0.318182 0.045455 0.181818 0.272727 0.454545 0.000000 0.272727 0.727273 0.136364 0.090909 0.045455 0.636364 0.272727 0.090909 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.909091 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.136364 0.590909 0.000000 0.272727 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CA[AC][AC][CAT]A[AC]CAAC[CT] -------------------------------------------------------------------------------- Time 11.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 13 llr = 187 E-value = 4.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:::211:::152:::22::: pos.-specific C :52::2::2::::::51:::3 probability G 444:8318175:329217187 matrix T 515a:582835558136192: bits 2.1 1.9 * 1.7 * 1.5 * * * Relative 1.3 ** ** ** ** Entropy 1.1 ** **** * ** *** (20.8 bits) 0.8 * ** **** * ** **** 0.6 **** ********* **** 0.4 ***** *************** 0.2 ********************* 0.0 --------------------- Multilevel TCTTGTTGTGGTTTGCTGTGG consensus GGG G T TTAG TAA C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25262 324 1.10e-11 AGGGGACATA TCGTGGTGTGTTTTGCTGTGG CATGTATTGC 10976 235 1.27e-09 GTCGTTTGAT TGTTGTTGTGTAGTGTAGTGG AGGAAGAAGT 2646 382 7.11e-09 GCAGCCACGC TCGTGTTGCGTTTTGCGGTGG TGGTGTTTCT 39913 60 1.97e-08 ATCCGGAGAA GCCTGTTTTGTATTGCCGTGG TCCCTTTGAT 7313 97 2.70e-08 TTGCTTGTTG GCTTGGTTTGGTTTGGTTTGG TTAGCGCGTA 37564 301 7.76e-08 GAGCTAGCGA GCGTATTGTGGAAGGTTGTGG GAGACACATT 21819 223 1.54e-07 TCGACATCTT GGTTGTTTCTTTGTGTTATGG GACGTGTTCT 24464 139 1.67e-07 ATGTTGGTGC AGCTGGTGTTGTTTGGTATGC TGCTCTCTTT 10523 236 3.87e-07 GTTGGTGCCA TTTTGTTGGGTTGTTCTGTGG TTGTGAAGGG 11454 118 5.12e-07 AGCATGGTCA TCTTGCGGTGGATTGCTGGTG ACGAAGGCGA 7153 128 8.12e-07 GTTGAAGACA AGGTGGAGTTGTTGGTTGTGC TACTACACAT 12021 271 8.65e-07 GTTATCGTTC GGGTACTGTGGAGTGGAGTTC CAGTCCAGCG 21033 156 1.04e-06 GATTGCAATT TCTTGATGTTAAATGCAATGC AGAGACGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25262 1.1e-11 323_[+3]_156 10976 1.3e-09 234_[+3]_245 2646 7.1e-09 381_[+3]_98 39913 2e-08 59_[+3]_420 7313 2.7e-08 96_[+3]_383 37564 7.8e-08 300_[+3]_179 21819 1.5e-07 222_[+3]_257 24464 1.7e-07 138_[+3]_341 10523 3.9e-07 235_[+3]_244 11454 5.1e-07 117_[+3]_362 7153 8.1e-07 127_[+3]_352 12021 8.6e-07 270_[+3]_209 21033 1e-06 155_[+3]_324 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=13 25262 ( 324) TCGTGGTGTGTTTTGCTGTGG 1 10976 ( 235) TGTTGTTGTGTAGTGTAGTGG 1 2646 ( 382) TCGTGTTGCGTTTTGCGGTGG 1 39913 ( 60) GCCTGTTTTGTATTGCCGTGG 1 7313 ( 97) GCTTGGTTTGGTTTGGTTTGG 1 37564 ( 301) GCGTATTGTGGAAGGTTGTGG 1 21819 ( 223) GGTTGTTTCTTTGTGTTATGG 1 24464 ( 139) AGCTGGTGTTGTTTGGTATGC 1 10523 ( 236) TTTTGTTGGGTTGTTCTGTGG 1 11454 ( 118) TCTTGCGGTGGATTGCTGGTG 1 7153 ( 128) AGGTGGAGTTGTTGGTTGTGC 1 12021 ( 271) GGGTACTGTGGAGTGGAGTTC 1 21033 ( 156) TCTTGATGTTAAATGCAATGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.4909 E= 4.3e-003 -75 -1035 60 84 -1035 122 60 -174 -1035 -58 60 84 -1035 -1035 -1035 196 -75 -1035 174 -1035 -174 -58 28 84 -174 -1035 -172 172 -1035 -1035 160 -16 -1035 -58 -172 158 -1035 -1035 145 26 -174 -1035 86 84 84 -1035 -1035 106 -75 -1035 28 106 -1035 -1035 -72 172 -1035 -1035 186 -174 -1035 100 -14 26 -16 -158 -172 126 -16 -1035 145 -174 -1035 -1035 -172 184 -1035 -1035 174 -74 -1035 42 145 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 4.3e-003 0.153846 0.000000 0.384615 0.461538 0.000000 0.538462 0.384615 0.076923 0.000000 0.153846 0.384615 0.461538 0.000000 0.000000 0.000000 1.000000 0.153846 0.000000 0.846154 0.000000 0.076923 0.153846 0.307692 0.461538 0.076923 0.000000 0.076923 0.846154 0.000000 0.000000 0.769231 0.230769 0.000000 0.153846 0.076923 0.769231 0.000000 0.000000 0.692308 0.307692 0.076923 0.000000 0.461538 0.461538 0.461538 0.000000 0.000000 0.538462 0.153846 0.000000 0.307692 0.538462 0.000000 0.000000 0.153846 0.846154 0.000000 0.000000 0.923077 0.076923 0.000000 0.461538 0.230769 0.307692 0.230769 0.076923 0.076923 0.615385 0.230769 0.000000 0.692308 0.076923 0.000000 0.000000 0.076923 0.923077 0.000000 0.000000 0.846154 0.153846 0.000000 0.307692 0.692308 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG][CG][TG]TG[TG]T[GT]T[GT][GT][TA][TG]TG[CTG][TA][GA]TG[GC] -------------------------------------------------------------------------------- Time 17.13 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10027 1.19e-04 210_[+2(4.41e-06)]_36_\ [+1(1.32e-06)]_180_[+2(8.97e-05)]_29 10479 1.76e-01 478_[+2(4.16e-05)]_10 10523 9.74e-08 235_[+3(3.87e-07)]_51_\ [+1(1.32e-06)]_40_[+2(6.60e-06)]_29_[+2(9.60e-05)]_79 10976 3.33e-09 212_[+2(6.60e-06)]_10_\ [+3(1.27e-09)]_36_[+1(1.02e-05)]_188 11127 8.25e-04 10_[+2(7.45e-05)]_303_\ [+1(7.09e-07)]_154 11454 7.41e-06 19_[+3(5.46e-05)]_77_[+3(5.12e-07)]_\ 25_[+1(6.46e-06)]_316 12021 1.29e-07 270_[+3(8.65e-07)]_22_\ [+1(9.04e-05)]_37_[+1(4.47e-08)]_108 21033 1.43e-04 155_[+3(1.04e-06)]_204_\ [+1(2.03e-05)]_99 21339 7.06e-04 60_[+2(1.32e-05)]_337_\ [+1(3.33e-06)]_46_[+2(3.03e-05)]_12 21819 3.38e-04 222_[+3(1.54e-07)]_257 22776 3.91e-03 358_[+1(3.23e-07)]_121 24132 4.02e-02 483_[+2(3.52e-05)]_5 24464 3.74e-06 50_[+3(3.08e-06)]_67_[+3(1.67e-07)]_\ 85_[+1(1.36e-05)]_185_[+2(8.57e-05)]_38 24491 6.31e-05 17_[+2(2.09e-05)]_52_[+1(2.87e-07)]_\ 398 25262 3.90e-10 80_[+2(3.06e-06)]_231_\ [+3(1.10e-11)]_156 25505 8.04e-05 248_[+2(8.62e-06)]_214_\ [+1(2.55e-06)]_5 25808 2.15e-03 141_[+2(5.21e-05)]_86_\ [+1(1.02e-05)]_240 264533 2.41e-03 488_[+2(9.49e-08)] 2646 2.19e-06 381_[+3(7.11e-09)]_70_\ [+1(7.55e-06)]_7 37564 9.46e-09 300_[+3(7.76e-08)]_103_\ [+1(6.11e-05)]_7_[+1(9.72e-07)]_15_[+2(3.49e-06)] 39913 1.16e-07 59_[+3(1.97e-08)]_282_\ [+1(4.19e-05)]_100_[+2(4.95e-06)]_5 6426 1.75e-03 201_[+2(1.94e-05)]_69_\ [+1(2.17e-05)]_197 6534 3.65e-06 57_[+1(2.12e-06)]_386_\ [+2(5.00e-08)]_24 7153 6.51e-07 127_[+3(8.12e-07)]_132_\ [+1(1.45e-06)]_148_[+2(2.32e-05)]_39 7311 2.09e-05 411_[+1(5.17e-10)]_68 7313 7.35e-12 96_[+3(2.70e-08)]_162_\ [+2(8.62e-06)]_120_[+1(5.17e-10)]_68 9911 4.19e-05 16_[+1(1.76e-06)]_408_\ [+2(7.52e-06)]_15_[+2(9.60e-05)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************