******************************************************************************** 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/287/287.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 105 1.0000 500 11836 1.0000 500 21291 1.0000 500 21723 1.0000 500 21863 1.0000 500 21905 1.0000 500 22749 1.0000 500 23232 1.0000 500 23452 1.0000 500 2350 1.0000 500 24127 1.0000 500 262414 1.0000 500 268519 1.0000 500 27997 1.0000 500 29166 1.0000 500 32108 1.0000 500 32137 1.0000 500 33653 1.0000 500 3904 1.0000 500 39187 1.0000 500 41014 1.0000 500 41178 1.0000 500 93 1.0000 500 9716 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/287/287.seqs.fa -oc motifs/287 -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= 24 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= 12000 N= 24 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.243 G 0.237 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.243 G 0.237 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 24 llr = 240 E-value = 1.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 22::646::534:732 pos.-specific C 835934259:81a238 probability G :3:1::2::::::11: matrix T :25:12:5:4:5::31 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * Relative 1.2 * * * * * Entropy 1.0 * ** ** * * * (14.4 bits) 0.8 * ** **** ** * 0.6 * ** ******* * 0.4 * ************ * 0.2 * ************** 0.0 ---------------- Multilevel CCCCAAATCACTCAAC consensus GT CCCC TAA C sequence A T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 21905 391 2.96e-07 CTCCCCGCCA CCTCTCATCACACAAC ACTAAGTTTA 41178 391 5.07e-07 TCGCCATCGT CACCATACCTCTCACC TTCATCCGTC 2350 479 7.94e-07 AACTCGTCGC CGTCCTACCACACACC CGTACC 93 484 9.06e-07 ACTGCATCGC CACCAAATCTCTCAGC C 262414 160 1.03e-06 CCGATCAACC CTCCACACCACACAAA CCATCCGCTC 41014 327 1.32e-06 TTGCACTATC CACCACATCACTCGTC TTCTTCTTCC 3904 103 1.91e-06 AGTTGCAAAT CTCCCAACCAAACAAC TGACGGTACA 9716 353 2.17e-06 TCCTCACTCA CCTCAAATCAACCATC AACATCTCCT 27997 465 2.79e-06 CCCTTCACAG CCCCACGTCTCTCCTC GTGTTTACGC 11836 453 3.55e-06 CCCTCCCACC CATCACACCAAACCCC AACGCAACTT 23452 445 4.43e-06 CTTCCACTCC CTTCCAACCTCTCCTC CAACACAACT 33653 428 6.60e-06 CACGTGTCCT CCTCAAGCCTCTCACT CCTGCATCGT 29166 471 6.60e-06 CATCTGCCAC CTCCCTGCCACTCATC TTTTCGCCAC 23232 331 9.64e-06 CCGCCACCGC CGCCAAACCACTCCAT CATCACGCTC 21863 83 9.64e-06 TGATAGGCTG ACTCAAGTCAAACAAC TCCTCAATGG 105 460 1.28e-05 ACGACCGAAG CCTCTACTCTCTCGAC CTCACGTTGT 24127 228 1.40e-05 GATTAGAACA AGTCAACTCAAACATC AGAGCAATGA 21291 70 1.53e-05 CAGCCTCTCT CTCCACCTCTATCGAC ACTTCAGTTC 32137 428 1.81e-05 CTTGTCACGC CGCCCCACCGCCCACC GCTGATTCAT 22749 195 4.46e-05 GTATGTCGAC CCTCACCTGTCACAAA AACTCAGTTT 21723 370 5.82e-05 ATCCTAAGTC ACCCCTTTCTCACACC AACAACCATA 39187 440 6.60e-05 ATAGTCCTGC AGCCAAACTACCCACC ACTAGAAGTT 32108 241 8.90e-05 CTCCTCTCCA CATGTCCTCACACACA GTAGAACTTG 268519 425 1.94e-04 GTGATGGCAT CGTGGCATCTCTCAGA TTGGCATATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21905 3e-07 390_[+1]_94 41178 5.1e-07 390_[+1]_94 2350 7.9e-07 478_[+1]_6 93 9.1e-07 483_[+1]_1 262414 1e-06 159_[+1]_325 41014 1.3e-06 326_[+1]_158 3904 1.9e-06 102_[+1]_382 9716 2.2e-06 352_[+1]_132 27997 2.8e-06 464_[+1]_20 11836 3.5e-06 452_[+1]_32 23452 4.4e-06 444_[+1]_40 33653 6.6e-06 427_[+1]_57 29166 6.6e-06 470_[+1]_14 23232 9.6e-06 330_[+1]_154 21863 9.6e-06 82_[+1]_402 105 1.3e-05 459_[+1]_25 24127 1.4e-05 227_[+1]_257 21291 1.5e-05 69_[+1]_415 32137 1.8e-05 427_[+1]_57 22749 4.5e-05 194_[+1]_290 21723 5.8e-05 369_[+1]_115 39187 6.6e-05 439_[+1]_45 32108 8.9e-05 240_[+1]_244 268519 0.00019 424_[+1]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=24 21905 ( 391) CCTCTCATCACACAAC 1 41178 ( 391) CACCATACCTCTCACC 1 2350 ( 479) CGTCCTACCACACACC 1 93 ( 484) CACCAAATCTCTCAGC 1 262414 ( 160) CTCCACACCACACAAA 1 41014 ( 327) CACCACATCACTCGTC 1 3904 ( 103) CTCCCAACCAAACAAC 1 9716 ( 353) CCTCAAATCAACCATC 1 27997 ( 465) CCCCACGTCTCTCCTC 1 11836 ( 453) CATCACACCAAACCCC 1 23452 ( 445) CTTCCAACCTCTCCTC 1 33653 ( 428) CCTCAAGCCTCTCACT 1 29166 ( 471) CTCCCTGCCACTCATC 1 23232 ( 331) CGCCAAACCACTCCAT 1 21863 ( 83) ACTCAAGTCAAACAAC 1 105 ( 460) CCTCTACTCTCTCGAC 1 24127 ( 228) AGTCAACTCAAACATC 1 21291 ( 70) CTCCACCTCTATCGAC 1 32137 ( 428) CGCCCCACCGCCCACC 1 22749 ( 195) CCTCACCTGTCACAAA 1 21723 ( 370) ACCCCTTTCTCACACC 1 39187 ( 440) AGCCAAACTACCCACC 1 32108 ( 241) CATGTCCTCACACACA 1 268519 ( 425) CGTGGCATCTCTCAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11640 bayes= 8.91886 E= 1.0e-007 -64 178 -1123 -1123 -32 46 8 -32 -1123 104 -1123 94 -1123 192 -150 -1123 117 4 -250 -106 68 78 -1123 -65 117 -22 -51 -264 -1123 92 -1123 105 -1123 192 -250 -264 106 -1123 -250 68 -5 163 -1123 -1123 68 -96 -1123 81 -1123 204 -1123 -1123 145 -54 -92 -1123 36 46 -150 -6 -64 163 -1123 -164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 1.0e-007 0.166667 0.833333 0.000000 0.000000 0.208333 0.333333 0.250000 0.208333 0.000000 0.500000 0.000000 0.500000 0.000000 0.916667 0.083333 0.000000 0.583333 0.250000 0.041667 0.125000 0.416667 0.416667 0.000000 0.166667 0.583333 0.208333 0.166667 0.041667 0.000000 0.458333 0.000000 0.541667 0.000000 0.916667 0.041667 0.041667 0.541667 0.000000 0.041667 0.416667 0.250000 0.750000 0.000000 0.000000 0.416667 0.125000 0.000000 0.458333 0.000000 1.000000 0.000000 0.000000 0.708333 0.166667 0.125000 0.000000 0.333333 0.333333 0.083333 0.250000 0.166667 0.750000 0.000000 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[CGAT][CT]C[AC][AC][AC][TC]C[AT][CA][TA]CA[ACT]C -------------------------------------------------------------------------------- Time 4.96 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 20 llr = 206 E-value = 7.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2121:12143:::: pos.-specific C :131:4::31::1: probability G 174285:94:a1:8 matrix T 82272:8::7:992 bits 2.1 * 1.9 * 1.7 * * 1.5 * *** Relative 1.2 * ** **** Entropy 1.0 * ** **** (14.8 bits) 0.8 * * ** ***** 0.6 ** ***** ***** 0.4 ** *********** 0.2 ************** 0.0 -------------- Multilevel TGGTGGTGGTGTTG consensus CGTCA AA T sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 21723 144 4.38e-08 AAGACGATGG TGCTGCTGATGTTG TACACTTGGA 27997 68 7.76e-08 AGTGGTCCCC TGCTGCTGCTGTTG CTGCGGCTGG 22749 343 9.12e-08 CAAAGACTTG TGGTGGAGGTGTTG GAGGCGTTGT 33653 55 1.22e-07 TTCTTGTTGT TGTTGCTGCTGTTG CGTCTGGATG 11836 280 2.70e-06 TGTTGTTGTT GGGTTGTGATGTTG AGCAGCCGCC 29166 176 3.33e-06 GGACGGCAGT TAGTGCAGATGTTG GAAACATTCG 105 290 3.67e-06 GTGGTAGGAC AGGTGGAGGAGTTG AGCAGTGTTT 262414 354 4.51e-06 TTGCGGTTAG TGCGTGTGGAGTTG TTGACCGTGG 3904 308 6.05e-06 GATTGGGCGA TGTTGGTGGTGGTT TGATGAGGAC 24127 381 9.38e-06 TCCCGCAGTT TGGCGGTGCAGTTT CGGTAGCTTC 23452 93 9.38e-06 CCATTGTGGC TGGTTCTGGAGTCG ATTTGGAAGA 268519 462 1.11e-05 CTTGTACTTC TAGAGCTGATGTTG TTGCCTTCAT 23232 82 1.21e-05 TCGCTGTGGT TGTGGCTGCCGTTG CTCAACAGGT 21863 259 1.33e-05 TGTTCGTCGG TCATGGTGGTGTTT ATGAAAGTTG 2350 241 1.43e-05 TGTGTGTTCC TTTTGGTACTGTTG AGTGGAGTTG 9716 257 2.14e-05 GGATAAAGAT TTAGGATGATGTTG AAGCGAATAA 32137 277 2.14e-05 TTAGTAGAAA TGCTGGAAGTGTTT CTATTAATTG 39187 191 2.48e-05 TGGAAGGCGG AGGCGCTGATGGTG GGGGTTGGTC 32108 50 5.96e-05 TTCATAGAGG AGCGGATGGTGTCG AGAGACGATT 41014 152 7.14e-05 GCCATGGTTT GTATTGTGAAGTTG TGAGTGGGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21723 4.4e-08 143_[+2]_343 27997 7.8e-08 67_[+2]_419 22749 9.1e-08 342_[+2]_144 33653 1.2e-07 54_[+2]_432 11836 2.7e-06 279_[+2]_207 29166 3.3e-06 175_[+2]_311 105 3.7e-06 289_[+2]_197 262414 4.5e-06 353_[+2]_133 3904 6.1e-06 307_[+2]_179 24127 9.4e-06 380_[+2]_106 23452 9.4e-06 92_[+2]_394 268519 1.1e-05 461_[+2]_25 23232 1.2e-05 81_[+2]_405 21863 1.3e-05 258_[+2]_228 2350 1.4e-05 240_[+2]_246 9716 2.1e-05 256_[+2]_230 32137 2.1e-05 276_[+2]_210 39187 2.5e-05 190_[+2]_296 32108 6e-05 49_[+2]_437 41014 7.1e-05 151_[+2]_335 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=20 21723 ( 144) TGCTGCTGATGTTG 1 27997 ( 68) TGCTGCTGCTGTTG 1 22749 ( 343) TGGTGGAGGTGTTG 1 33653 ( 55) TGTTGCTGCTGTTG 1 11836 ( 280) GGGTTGTGATGTTG 1 29166 ( 176) TAGTGCAGATGTTG 1 105 ( 290) AGGTGGAGGAGTTG 1 262414 ( 354) TGCGTGTGGAGTTG 1 3904 ( 308) TGTTGGTGGTGGTT 1 24127 ( 381) TGGCGGTGCAGTTT 1 23452 ( 93) TGGTTCTGGAGTCG 1 268519 ( 462) TAGAGCTGATGTTG 1 23232 ( 82) TGTGGCTGCCGTTG 1 21863 ( 259) TCATGGTGGTGTTT 1 2350 ( 241) TTTTGGTACTGTTG 1 9716 ( 257) TTAGGATGATGTTG 1 32137 ( 277) TGCTGGAAGTGTTT 1 39187 ( 191) AGGCGCTGATGGTG 1 32108 ( 50) AGCGGATGGTGTCG 1 41014 ( 152) GTATTGTGAAGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 11688 bayes= 10.6639 E= 7.0e-005 -79 -1097 -124 152 -138 -228 156 -80 -79 4 76 -38 -237 -128 -24 132 -1097 -1097 176 -38 -138 72 108 -1097 -38 -1097 -1097 162 -138 -1097 193 -1097 43 4 76 -1097 -5 -228 -1097 142 -1097 -1097 208 -1097 -1097 -1097 -124 179 -1097 -128 -1097 179 -1097 -1097 176 -38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 20 E= 7.0e-005 0.150000 0.000000 0.100000 0.750000 0.100000 0.050000 0.700000 0.150000 0.150000 0.250000 0.400000 0.200000 0.050000 0.100000 0.200000 0.650000 0.000000 0.000000 0.800000 0.200000 0.100000 0.400000 0.500000 0.000000 0.200000 0.000000 0.000000 0.800000 0.100000 0.000000 0.900000 0.000000 0.350000 0.250000 0.400000 0.000000 0.250000 0.050000 0.000000 0.700000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[GCT][TG][GT][GC][TA]G[GAC][TA]GTT[GT] -------------------------------------------------------------------------------- Time 9.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 15 llr = 199 E-value = 3.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3335:2131:11:1185255: pos.-specific C :1::::::1::111:::1::: probability G 72359:55197:919256439 matrix T 144118336139:6:::1131 bits 2.1 1.9 1.7 * * 1.5 * * * * * Relative 1.2 ** * ** ** * Entropy 1.0 ** * ** *** * (19.1 bits) 0.8 * ** **** *** * 0.6 * **** **** *** * * 0.4 * ******************* 0.2 * ******************* 0.0 --------------------- Multilevel GTTAGTGGTGGTGTGAGGAAG consensus AAAG ATA T GAAGG sequence GG T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41178 138 4.10e-10 TGGTCGGGAG GTAGGTTGGGGTGTGAGGAAG GTGGAGAACA 21723 302 9.81e-09 CGCATCAGAA AGAAGTTGTGGTGTGGAGAAG GGAGGTATGT 27997 147 3.66e-08 TTGTTGTGGA GTTGGTGGATGTGAGAGGAAG AGGACAGTTA 21863 284 7.77e-08 TGAAAGTTGT GTTGGTTTTGGCGCGAAGAAG CCACGTGGAA 33653 203 9.52e-08 TGTGATTGGT GTAGGTGATGTTGAGAGGAGT GTATTGAGGC 105 5 1.28e-07 ATTG ATGTGTTGTGGTGTGGGGGTG ACTCAAGATA 3904 12 2.95e-07 AATGGGTGGT GGTAGTGATGGAGTGGAAGAG ATGAAAGAAC 23452 152 2.95e-07 ATGTGAGCTT GCTGGAGGTGGTCTGAGAAGG AAGAAGAAAG 39187 228 3.23e-07 CATGTCGAAA GCAATTGAGGGTGGGAGGGAG GGTATTTGTC 268519 149 8.01e-07 GGAAATCATT GAGGTAGTTGGTGTAAAGGAG GTCGATACTT 41014 79 9.35e-07 TGAGTGGTAT GATAGTAGTGATGCGAGTATG AACGAGAGGC 32108 135 1.09e-06 CAAATCTTTT TTTAGTGAAGTTGTGAATATG ATATACAATA 22749 416 1.09e-06 GACGAAGAAT AAAAGTTTCGTTGTGAAGTGG AACTTCTTCG 21291 239 1.80e-06 CATAGTTGTG AGGAGTGTTGTTGTGAACGGT GCACCAACGA 21905 7 5.69e-06 TTACTG GAGGGAAGCTGTGGGAGAGTG CTGAGCAAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41178 4.1e-10 137_[+3]_342 21723 9.8e-09 301_[+3]_178 27997 3.7e-08 146_[+3]_333 21863 7.8e-08 283_[+3]_196 33653 9.5e-08 202_[+3]_277 105 1.3e-07 4_[+3]_475 3904 3e-07 11_[+3]_468 23452 3e-07 151_[+3]_328 39187 3.2e-07 227_[+3]_252 268519 8e-07 148_[+3]_331 41014 9.3e-07 78_[+3]_401 32108 1.1e-06 134_[+3]_345 22749 1.1e-06 415_[+3]_64 21291 1.8e-06 238_[+3]_241 21905 5.7e-06 6_[+3]_473 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=15 41178 ( 138) GTAGGTTGGGGTGTGAGGAAG 1 21723 ( 302) AGAAGTTGTGGTGTGGAGAAG 1 27997 ( 147) GTTGGTGGATGTGAGAGGAAG 1 21863 ( 284) GTTGGTTTTGGCGCGAAGAAG 1 33653 ( 203) GTAGGTGATGTTGAGAGGAGT 1 105 ( 5) ATGTGTTGTGGTGTGGGGGTG 1 3904 ( 12) GGTAGTGATGGAGTGGAAGAG 1 23452 ( 152) GCTGGAGGTGGTCTGAGAAGG 1 39187 ( 228) GCAATTGAGGGTGGGAGGGAG 1 268519 ( 149) GAGGTAGTTGGTGTAAAGGAG 1 41014 ( 79) GATAGTAGTGATGCGAGTATG 1 32108 ( 135) TTTAGTGAAGTTGTGAATATG 1 22749 ( 416) AAAAGTTTCGTTGTGAAGTGG 1 21291 ( 239) AGGAGTGTTGTTGTGAACGGT 1 21905 ( 7) GAGGGAAGCTGTGGGAGAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11520 bayes= 10.258 E= 3.0e-003 4 -1055 149 -197 4 -86 -24 62 36 -1055 17 62 85 -1055 98 -197 -1055 -1055 187 -97 -38 -1055 -1055 162 -96 -1055 117 35 4 -1055 98 3 -96 -86 -83 120 -1055 -1055 187 -97 -196 -1055 149 3 -196 -186 -1055 173 -1055 -186 198 -1055 -96 -86 -83 120 -196 -1055 198 -1055 162 -1055 -24 -1055 85 -1055 117 -1055 -38 -186 134 -97 104 -1055 76 -197 85 -1055 17 3 -1055 -1055 187 -97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 15 E= 3.0e-003 0.266667 0.000000 0.666667 0.066667 0.266667 0.133333 0.200000 0.400000 0.333333 0.000000 0.266667 0.400000 0.466667 0.000000 0.466667 0.066667 0.000000 0.000000 0.866667 0.133333 0.200000 0.000000 0.000000 0.800000 0.133333 0.000000 0.533333 0.333333 0.266667 0.000000 0.466667 0.266667 0.133333 0.133333 0.133333 0.600000 0.000000 0.000000 0.866667 0.133333 0.066667 0.000000 0.666667 0.266667 0.066667 0.066667 0.000000 0.866667 0.000000 0.066667 0.933333 0.000000 0.133333 0.133333 0.133333 0.600000 0.066667 0.000000 0.933333 0.000000 0.800000 0.000000 0.200000 0.000000 0.466667 0.000000 0.533333 0.000000 0.200000 0.066667 0.600000 0.133333 0.533333 0.000000 0.400000 0.066667 0.466667 0.000000 0.266667 0.266667 0.000000 0.000000 0.866667 0.133333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][TAG][TAG][AG]G[TA][GT][GAT]TG[GT]TGTG[AG][GA][GA][AG][AGT]G -------------------------------------------------------------------------------- Time 14.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 105 1.66e-07 4_[+3(1.28e-07)]_264_[+2(3.67e-06)]_\ 156_[+1(1.28e-05)]_25 11836 3.82e-05 279_[+2(2.70e-06)]_159_\ [+1(3.55e-06)]_32 21291 4.85e-04 69_[+1(1.53e-05)]_153_\ [+3(1.80e-06)]_241 21723 1.07e-09 143_[+2(4.38e-08)]_144_\ [+3(9.81e-09)]_47_[+1(5.82e-05)]_115 21863 2.64e-07 82_[+1(9.64e-06)]_160_\ [+2(1.33e-05)]_11_[+3(7.77e-08)]_196 21905 2.90e-05 6_[+3(5.69e-06)]_363_[+1(2.96e-07)]_\ 59_[+1(5.46e-05)]_19 22749 1.25e-07 194_[+1(4.46e-05)]_132_\ [+2(9.12e-08)]_59_[+3(1.09e-06)]_64 23232 1.53e-03 81_[+2(1.21e-05)]_235_\ [+1(9.64e-06)]_154 23452 3.19e-07 92_[+2(9.38e-06)]_45_[+3(2.95e-07)]_\ 272_[+1(4.43e-06)]_40 2350 9.66e-05 147_[+2(8.05e-05)]_79_\ [+2(1.43e-05)]_224_[+1(7.94e-07)]_6 24127 1.24e-03 227_[+1(1.40e-05)]_137_\ [+2(9.38e-06)]_106 262414 6.76e-05 71_[+2(2.84e-05)]_74_[+1(1.03e-06)]_\ 178_[+2(4.51e-06)]_133 268519 2.55e-05 148_[+3(8.01e-07)]_292_\ [+2(1.11e-05)]_25 27997 3.72e-10 67_[+2(7.76e-08)]_65_[+3(3.66e-08)]_\ 297_[+1(2.79e-06)]_20 29166 4.01e-05 175_[+2(3.33e-06)]_281_\ [+1(6.60e-06)]_14 32108 7.40e-05 49_[+2(5.96e-05)]_71_[+3(1.09e-06)]_\ 85_[+1(8.90e-05)]_244 32137 1.88e-03 276_[+2(2.14e-05)]_137_\ [+1(1.81e-05)]_57 33653 3.05e-09 54_[+2(1.22e-07)]_134_\ [+3(9.52e-08)]_204_[+1(6.60e-06)]_57 3904 9.98e-08 11_[+3(2.95e-07)]_70_[+1(1.91e-06)]_\ 189_[+2(6.05e-06)]_179 39187 9.15e-06 190_[+2(2.48e-05)]_23_\ [+3(3.23e-07)]_191_[+1(6.60e-05)]_45 41014 1.86e-06 78_[+3(9.35e-07)]_53_[+3(5.37e-06)]_\ 153_[+1(1.32e-06)]_158 41178 4.99e-09 137_[+3(4.10e-10)]_232_\ [+1(5.07e-07)]_94 93 1.52e-02 483_[+1(9.06e-07)]_1 9716 4.73e-04 137_[+1(2.48e-05)]_103_\ [+2(2.14e-05)]_82_[+1(2.17e-06)]_132 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************