******************************************************************************** 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/234/234.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9319 1.0000 500 42636 1.0000 500 8828 1.0000 500 20837 1.0000 500 54597 1.0000 500 46741 1.0000 500 37615 1.0000 500 42169 1.0000 500 573 1.0000 500 18345 1.0000 500 33016 1.0000 500 43770 1.0000 500 49524 1.0000 500 10319 1.0000 500 33839 1.0000 500 7639 1.0000 500 11230 1.0000 500 44938 1.0000 500 11799 1.0000 500 7335 1.0000 500 8270 1.0000 500 45697 1.0000 500 12366 1.0000 500 36139 1.0000 500 46285 1.0000 500 31763 1.0000 500 44274 1.0000 500 43283 1.0000 500 49668 1.0000 500 47477 1.0000 500 48058 1.0000 500 38166 1.0000 500 40347 1.0000 500 39648 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/234/234.seqs.fa -oc motifs/234 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.252 C 0.264 G 0.238 T 0.245 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.264 G 0.238 T 0.245 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 20 llr = 220 E-value = 4.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 41::3261:17:6311 pos.-specific C 3735272::a:a:::a probability G :3234113::2117:: matrix T 4:632:27a:2:4:a: bits 2.1 * 1.9 * 1.7 ** * ** 1.4 ** * ** Relative 1.2 ** * *** Entropy 1.0 ** * *** (15.9 bits) 0.8 * * ********* 0.6 ** * ********* 0.4 **** *********** 0.2 **** *********** 0.0 ---------------- Multilevel ACTCGCATTCACAGTC consensus TGCGAACG TA sequence C GTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 49524 50 2.82e-08 TTCGAGTGCG ACTCACAGTCACTGTC AAATCCAGTC 44938 198 3.33e-08 AAATCGACAA TCCTGCATTCACAGTC AACGTGGAGT 47477 100 1.97e-07 CTTGGTTCGA TCGGCCATTCACAGTC ATACCCGAAC 54597 244 4.64e-07 AACCCAGATG TCCGACCTTCACAGTC GTTTGCGACA 40347 132 5.29e-07 CGTTTGGCGC CGTCCCATTCACTATC GATAACGGCT 12366 207 6.76e-07 GCGCAGTCGT TCCCGCAGTCGCAGTC CCGGCGCTCC 48058 467 9.67e-07 GATCGAGTCA ACTTAATTTCACAGTC CGTACTTCGT 33016 215 1.85e-06 TCGGGATTTC TCTGTCGTTCACAGTC ACGTCACACT 7335 478 2.27e-06 AGATCATTCT CATCGGATTCACTGTC CGCCGAA 7639 63 2.27e-06 ACCATGCTCA CGTCACCGTCACAATC CGTGTTTCTT 8828 280 4.71e-06 ACGTTTCGGG ACTCGCATTCTCTGTA GGAATGGCCG 46741 432 5.56e-06 GATTGACTGT AATTGCAATCACAGTC GTAATCGTAG 39648 155 6.52e-06 CGTCCGTCGA ACTCCAATTCACTGAC TGACAGTGAG 31763 94 7.63e-06 ACATCCAATT TCCTGCAGTCACGATC ACATATAACA 44274 229 1.18e-05 TCGGCGATGA ACGGACCTTCAGAGTC TGTCCGTATA 10319 268 1.18e-05 CTACCGTCGT CGTTGCCGTCTCAATC TGCTCGGAAT 49668 186 1.36e-05 TGGAGACAAC CCGGTGTTTCACTGTC AGTAAGGCAA 33839 75 1.66e-05 ATCTTAAATA CCCCCAAGTCGCTATC CAAAATTTGT 43770 459 2.27e-05 TTGCACACAC TGGCTATTTCGCAGTC GACGAGAGAA 42169 150 2.27e-05 GCAGTCTTTT AGTCACATTATCTATC CATAGATTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49524 2.8e-08 49_[+1]_435 44938 3.3e-08 197_[+1]_287 47477 2e-07 99_[+1]_385 54597 4.6e-07 243_[+1]_241 40347 5.3e-07 131_[+1]_353 12366 6.8e-07 206_[+1]_278 48058 9.7e-07 466_[+1]_18 33016 1.9e-06 214_[+1]_270 7335 2.3e-06 477_[+1]_7 7639 2.3e-06 62_[+1]_422 8828 4.7e-06 279_[+1]_205 46741 5.6e-06 431_[+1]_53 39648 6.5e-06 154_[+1]_330 31763 7.6e-06 93_[+1]_391 44274 1.2e-05 228_[+1]_256 10319 1.2e-05 267_[+1]_217 49668 1.4e-05 185_[+1]_299 33839 1.7e-05 74_[+1]_410 43770 2.3e-05 458_[+1]_26 42169 2.3e-05 149_[+1]_335 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=20 49524 ( 50) ACTCACAGTCACTGTC 1 44938 ( 198) TCCTGCATTCACAGTC 1 47477 ( 100) TCGGCCATTCACAGTC 1 54597 ( 244) TCCGACCTTCACAGTC 1 40347 ( 132) CGTCCCATTCACTATC 1 12366 ( 207) TCCCGCAGTCGCAGTC 1 48058 ( 467) ACTTAATTTCACAGTC 1 33016 ( 215) TCTGTCGTTCACAGTC 1 7335 ( 478) CATCGGATTCACTGTC 1 7639 ( 63) CGTCACCGTCACAATC 1 8828 ( 280) ACTCGCATTCTCTGTA 1 46741 ( 432) AATTGCAATCACAGTC 1 39648 ( 155) ACTCCAATTCACTGAC 1 31763 ( 94) TCCTGCAGTCACGATC 1 44274 ( 229) ACGGACCTTCAGAGTC 1 10319 ( 268) CGTTGCCGTCTCAATC 1 49668 ( 186) CCGGTGTTTCACTGTC 1 33839 ( 75) CCCCCAAGTCGCTATC 1 43770 ( 459) TGGCTATTTCGCAGTC 1 42169 ( 150) AGTCACATTATCTATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16490 bayes= 10.6299 E= 4.6e-002 47 18 -1097 51 -133 130 7 -1097 -1097 -8 -25 116 -1097 92 7 3 25 -40 55 -71 -33 141 -125 -1097 125 -40 -225 -71 -233 -1097 33 141 -1097 -1097 -1097 203 -233 185 -1097 -1097 147 -1097 -67 -71 -1097 185 -225 -1097 112 -1097 -225 70 25 -1097 155 -1097 -233 -1097 -1097 195 -233 185 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 4.6e-002 0.350000 0.300000 0.000000 0.350000 0.100000 0.650000 0.250000 0.000000 0.000000 0.250000 0.200000 0.550000 0.000000 0.500000 0.250000 0.250000 0.300000 0.200000 0.350000 0.150000 0.200000 0.700000 0.100000 0.000000 0.600000 0.200000 0.050000 0.150000 0.050000 0.000000 0.300000 0.650000 0.000000 0.000000 0.000000 1.000000 0.050000 0.950000 0.000000 0.000000 0.700000 0.000000 0.150000 0.150000 0.000000 0.950000 0.050000 0.000000 0.550000 0.000000 0.050000 0.400000 0.300000 0.000000 0.700000 0.000000 0.050000 0.000000 0.000000 0.950000 0.050000 0.950000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ATC][CG][TCG][CGT][GAC][CA][AC][TG]TCAC[AT][GA]TC -------------------------------------------------------------------------------- Time 10.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 13 llr = 183 E-value = 1.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:::1::12:44321:21::1 pos.-specific C :1:8::::25:15:5:52133 probability G 12:17::25562:22113:16 matrix T 87a22aa72::327292496: bits 2.1 * ** 1.9 * ** 1.7 * ** * * 1.4 * ** * * Relative 1.2 * * ** * * Entropy 1.0 * ** ** ** * * (20.3 bits) 0.8 ******** ** * * *** 0.6 ******** ** * * *** 0.4 ******** ** ** * *** 0.2 ********************* 0.0 --------------------- Multilevel TTTCGTTTGGGACTCTCTTTG consensus G T GTCATA T TG CC sequence GT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44938 108 4.28e-09 GCAGTCATCG TGTCGTTGGCAGATCTCTTTG TCGAACGGTT 43283 289 2.04e-08 ATAATTGATA TTTCATTTGCGTATCTGTTTG TCAACCCGAA 40347 423 3.48e-08 TTTCCACCAG TTTCGTTTCGGCTTGTTTTTG TTGAATCTGG 33016 284 3.86e-08 CTCCGCCTTT TTTTGTTTTGAGCTCTCCTCC TCCTTTCCCA 10319 340 6.33e-08 GATTCCTCGT TTTCGTTAACGAATTTATTTG CCAAAACCGC 38166 296 1.01e-07 ATCTCGCGAG TGTCTTTTGGGACTCTTTCCG ATACGCGTAG 42636 199 1.01e-07 CGAGGTTGAT TTTCGTTGTCAACGCTCGTTA CGGTCGACGA 45697 405 1.11e-07 TCTGATTGTG TCTCGTTTGGGACTATCGTGG ACCTCTCGGC 7335 322 2.02e-07 AACGTTGTCC TTTCTTTGGGATTTCGCGTCG GAGACCAACG 8828 108 2.80e-07 GGCTGCCATT TTTCGTTTCCGGTATTCATTC CAGGTGTTTC 37615 225 4.43e-07 TCCATTTTTC TTTGGTTTGCGTCGGTACTCG AATCCGCCGT 33839 95 5.12e-07 GCTATCCAAA ATTTGTTTTGAAAACTCGTTC TTAAATCCAA 46285 136 1.08e-06 TATCTTCGGG GGTCTTTTAGGTCTTTTCTTC GATGACTCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44938 4.3e-09 107_[+2]_372 43283 2e-08 288_[+2]_191 40347 3.5e-08 422_[+2]_57 33016 3.9e-08 283_[+2]_196 10319 6.3e-08 339_[+2]_140 38166 1e-07 295_[+2]_184 42636 1e-07 198_[+2]_281 45697 1.1e-07 404_[+2]_75 7335 2e-07 321_[+2]_158 8828 2.8e-07 107_[+2]_372 37615 4.4e-07 224_[+2]_255 33839 5.1e-07 94_[+2]_385 46285 1.1e-06 135_[+2]_344 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=13 44938 ( 108) TGTCGTTGGCAGATCTCTTTG 1 43283 ( 289) TTTCATTTGCGTATCTGTTTG 1 40347 ( 423) TTTCGTTTCGGCTTGTTTTTG 1 33016 ( 284) TTTTGTTTTGAGCTCTCCTCC 1 10319 ( 340) TTTCGTTAACGAATTTATTTG 1 38166 ( 296) TGTCTTTTGGGACTCTTTCCG 1 42636 ( 199) TTTCGTTGTCAACGCTCGTTA 1 45697 ( 405) TCTCGTTTGGGACTATCGTGG 1 7335 ( 322) TTTCTTTGGGATTTCGCGTCG 1 8828 ( 108) TTTCGTTTCCGGTATTCATTC 1 37615 ( 225) TTTGGTTTGCGTCGGTACTCG 1 33839 ( 95) ATTTGTTTTGAAAACTCGTTC 1 46285 ( 136) GGTCTTTTAGGTCTTTTCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 11.4578 E= 1.0e+000 -171 -1035 -163 179 -1035 -178 -5 150 -1035 -1035 -1035 203 -1035 154 -163 -67 -171 -1035 154 -9 -1035 -1035 -1035 203 -1035 -1035 -1035 203 -171 -1035 -5 150 -71 -78 95 -9 -1035 81 117 -1035 61 -1035 137 -1035 61 -178 -5 33 29 81 -1035 -9 -71 -1035 -63 150 -171 103 -63 -9 -1035 -1035 -163 191 -71 103 -163 -9 -171 -19 37 65 -1035 -178 -1035 191 -1035 22 -163 133 -171 22 137 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 10.0e-001 0.076923 0.000000 0.076923 0.846154 0.000000 0.076923 0.230769 0.692308 0.000000 0.000000 0.000000 1.000000 0.000000 0.769231 0.076923 0.153846 0.076923 0.000000 0.692308 0.230769 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.076923 0.000000 0.230769 0.692308 0.153846 0.153846 0.461538 0.230769 0.000000 0.461538 0.538462 0.000000 0.384615 0.000000 0.615385 0.000000 0.384615 0.076923 0.230769 0.307692 0.307692 0.461538 0.000000 0.230769 0.153846 0.000000 0.153846 0.692308 0.076923 0.538462 0.153846 0.230769 0.000000 0.000000 0.076923 0.923077 0.153846 0.538462 0.076923 0.230769 0.076923 0.230769 0.307692 0.384615 0.000000 0.076923 0.000000 0.923077 0.000000 0.307692 0.076923 0.615385 0.076923 0.307692 0.615385 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[TG]TC[GT]TT[TG][GT][GC][GA][ATG][CAT]T[CT]T[CT][TGC]T[TC][GC] -------------------------------------------------------------------------------- Time 19.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 34 llr = 294 E-value = 1.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2442345397229876 pos.-specific C 61:47416117412:4 probability G 2:51:241:1:51:1: matrix T :413::::::1:::1: bits 2.1 1.9 1.7 1.4 * Relative 1.2 * ** Entropy 1.0 * * ** (12.5 bits) 0.8 * ** **** 0.6 *** * ********** 0.4 *** ************ 0.2 **************** 0.0 ---------------- Multilevel CTGCCAACAACGAAAA consensus GAATACGA C C C sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11230 439 2.84e-07 GGTCCCACTG CAGACGAAAACGAAAA CGACGAAAGC 8828 52 7.71e-07 ATACTTTTTG CTGCCAGCAACAACAA ACAGGTCGAA 49524 359 8.85e-07 TCCTACCATC CTACCAACAAACAAAC ACAGGGAACG 48058 438 1.03e-06 AAAATGGCAC CTTTCAGCAACCAAAA ATCGATCGAG 33016 434 1.61e-06 TAGATCAACA CAGCACGGAACGAAAC GACACGGCGT 46741 277 1.61e-06 TTGGTGCTCA CTGTCCGCCACCAAAA TGGACCTGCC 42636 459 2.80e-06 GCATGGATGG CAGGCAGGAACGAAAA AGTCGCCGTG 7335 104 3.18e-06 GGGATCGTCT GTGCCCAAAACCACAA AATGTGATGT 43770 81 3.62e-06 GGAATGTTCA CAGTCGGCAATGAAAC CCATCGCAAA 40347 351 4.13e-06 CAAAAAGACC CAAAAAACAACAAAAC AGAGAATGTC 39648 468 5.29e-06 GGCAAGTAAG ACAACGACAACGAAAA CCGTCACCGT 37615 306 6.72e-06 TATTCACTGT CAGCCAACACCCAAGA TCACCAACCT 9319 357 8.53e-06 AGTTTCTTTG GCGCCCAAAAAGAAAA CGAACGATAG 44274 474 1.06e-05 GCAACAGCAA AAGCCCTCAACCAAAA ACACCTTCCT 42169 244 1.19e-05 GGACTCCACA GTGCCCGAAATCAAAC AAGGGTTTTC 46285 14 1.33e-05 TTCCCATTCC GTTCCAGCAACGACAC CGAGGCCAGC 38166 218 1.82e-05 CCCGTGTCGA GAAACAACACCAAAAA AGCCACGTTC 49668 6 2.47e-05 CCGTA CAATACACAAGGAAAA GGCTCCTTTC 33839 263 4.80e-05 ATTTCGGGCT CCGTCCAAAACAAATC GACTAGTACG 18345 379 5.74e-05 CCCACCAGAG GTGAACACAGACAAAA CCGTAATGGG 54597 148 7.43e-05 GATTGTTGCA ACGAAGACAACGAATA ACAAATAGTC 43283 311 8.78e-05 ATCTGTTTGT CAACCCGAAGTGACAA AGAGCTTGCG 10319 70 8.78e-05 GAGCAAGACC GAAGCAGAAACCAAGC TGTGTTTGTG 573 275 8.78e-05 ATCCACCCTC GTATCAACAACAGCAA ACTCCGCAGC 36139 442 9.52e-05 ACAACTACCA ATACCCAGCACGAAGA GGACGTAGCG 45697 459 9.52e-05 GCCTGCCTGC CTGCCAAGCACCCAAA CCACATTCCA 44938 483 1.41e-04 TATTCTCTAA CTGTAAGCAGCGGCAA CC 11799 48 2.04e-04 GCGCCCCGTC CATCCGACATCGACAC ATACTCGTAG 20837 193 2.04e-04 TACCGATGTG ATATAAGCAGCCAATC CAGTCAGCTT 47477 141 2.18e-04 TCCCACGAAT CCACACGAACCGAATC GAGTAAAACC 8270 175 2.34e-04 CCCAAGGAAG ATGTCCCCAAAAAAGA ACGCAGGGAA 7639 193 3.27e-04 GTGGCTACTA CAGACGGCAAACGAAT CACTCTCCCT 12366 245 5.35e-04 CCCGTCGTTC CTACCGGGACCGCAGC TACAGTCCGT 31763 322 6.71e-04 GATGCTGCTT CAAAAGCACAAGAAAC CCATTGGGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11230 2.8e-07 438_[+3]_46 8828 7.7e-07 51_[+3]_433 49524 8.9e-07 358_[+3]_126 48058 1e-06 437_[+3]_47 33016 1.6e-06 433_[+3]_51 46741 1.6e-06 276_[+3]_208 42636 2.8e-06 458_[+3]_26 7335 3.2e-06 103_[+3]_381 43770 3.6e-06 80_[+3]_404 40347 4.1e-06 350_[+3]_134 39648 5.3e-06 467_[+3]_17 37615 6.7e-06 305_[+3]_179 9319 8.5e-06 356_[+3]_128 44274 1.1e-05 473_[+3]_11 42169 1.2e-05 243_[+3]_241 46285 1.3e-05 13_[+3]_471 38166 1.8e-05 217_[+3]_267 49668 2.5e-05 5_[+3]_479 33839 4.8e-05 262_[+3]_222 18345 5.7e-05 378_[+3]_106 54597 7.4e-05 147_[+3]_337 43283 8.8e-05 310_[+3]_174 10319 8.8e-05 69_[+3]_415 573 8.8e-05 274_[+3]_210 36139 9.5e-05 441_[+3]_43 45697 9.5e-05 458_[+3]_26 44938 0.00014 482_[+3]_2 11799 0.0002 47_[+3]_437 20837 0.0002 192_[+3]_292 47477 0.00022 140_[+3]_344 8270 0.00023 174_[+3]_310 7639 0.00033 192_[+3]_292 12366 0.00054 244_[+3]_240 31763 0.00067 321_[+3]_163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=34 11230 ( 439) CAGACGAAAACGAAAA 1 8828 ( 52) CTGCCAGCAACAACAA 1 49524 ( 359) CTACCAACAAACAAAC 1 48058 ( 438) CTTTCAGCAACCAAAA 1 33016 ( 434) CAGCACGGAACGAAAC 1 46741 ( 277) CTGTCCGCCACCAAAA 1 42636 ( 459) CAGGCAGGAACGAAAA 1 7335 ( 104) GTGCCCAAAACCACAA 1 43770 ( 81) CAGTCGGCAATGAAAC 1 40347 ( 351) CAAAAAACAACAAAAC 1 39648 ( 468) ACAACGACAACGAAAA 1 37615 ( 306) CAGCCAACACCCAAGA 1 9319 ( 357) GCGCCCAAAAAGAAAA 1 44274 ( 474) AAGCCCTCAACCAAAA 1 42169 ( 244) GTGCCCGAAATCAAAC 1 46285 ( 14) GTTCCAGCAACGACAC 1 38166 ( 218) GAAACAACACCAAAAA 1 49668 ( 6) CAATACACAAGGAAAA 1 33839 ( 263) CCGTCCAAAACAAATC 1 18345 ( 379) GTGAACACAGACAAAA 1 54597 ( 148) ACGAAGACAACGAATA 1 43283 ( 311) CAACCCGAAGTGACAA 1 10319 ( 70) GAAGCAGAAACCAAGC 1 573 ( 275) GTATCAACAACAGCAA 1 36139 ( 442) ATACCCAGCACGAAGA 1 45697 ( 459) CTGCCAAGCACCCAAA 1 44938 ( 483) CTGTAAGCAGCGGCAA 1 11799 ( 48) CATCCGACATCGACAC 1 20837 ( 193) ATATAAGCAGCCAATC 1 47477 ( 141) CCACACGAACCGAATC 1 8270 ( 175) ATGTCCCCAAAAAAGA 1 7639 ( 193) CAGACGGCAAACGAAT 1 12366 ( 245) CTACCGGGACCGCAGC 1 31763 ( 322) CAAAAGCACAAGAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16490 bayes= 8.98854 E= 1.9e+000 -51 116 -2 -1173 71 -84 -1173 85 60 -1173 115 -147 -10 74 -202 11 7 148 -1173 -1173 60 53 -2 -1173 90 -216 89 -306 7 116 -70 -1173 181 -117 -1173 -1173 154 -117 -102 -306 -51 142 -302 -147 -51 42 98 -1173 176 -216 -143 -1173 165 -36 -1173 -1173 154 -1173 -70 -106 122 53 -1173 -306 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 34 E= 1.9e+000 0.176471 0.588235 0.235294 0.000000 0.411765 0.147059 0.000000 0.441176 0.382353 0.000000 0.529412 0.088235 0.235294 0.441176 0.058824 0.264706 0.264706 0.735294 0.000000 0.000000 0.382353 0.382353 0.235294 0.000000 0.470588 0.058824 0.441176 0.029412 0.264706 0.588235 0.147059 0.000000 0.882353 0.117647 0.000000 0.000000 0.735294 0.117647 0.117647 0.029412 0.176471 0.705882 0.029412 0.088235 0.176471 0.352941 0.470588 0.000000 0.852941 0.058824 0.088235 0.000000 0.794118 0.205882 0.000000 0.000000 0.735294 0.000000 0.147059 0.117647 0.588235 0.382353 0.000000 0.029412 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][TA][GA][CTA][CA][ACG][AG][CA]AAC[GC]A[AC]A[AC] -------------------------------------------------------------------------------- Time 29.58 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9319 2.95e-02 356_[+3(8.53e-06)]_128 42636 8.69e-06 198_[+2(1.01e-07)]_239_\ [+3(2.80e-06)]_26 8828 3.27e-08 51_[+3(7.71e-07)]_40_[+2(2.80e-07)]_\ 151_[+1(4.71e-06)]_205 20837 2.77e-01 500 54597 2.02e-04 147_[+3(7.43e-05)]_80_\ [+1(4.64e-07)]_241 46741 1.06e-04 276_[+3(1.61e-06)]_139_\ [+1(5.56e-06)]_53 37615 6.15e-05 224_[+2(4.43e-07)]_60_\ [+3(6.72e-06)]_179 42169 1.71e-03 149_[+1(2.27e-05)]_78_\ [+3(1.19e-05)]_241 573 2.66e-01 274_[+3(8.78e-05)]_210 18345 1.53e-01 378_[+3(5.74e-05)]_106 33016 4.44e-09 214_[+1(1.85e-06)]_53_\ [+2(3.86e-08)]_129_[+3(1.61e-06)]_51 43770 3.94e-04 80_[+3(3.62e-06)]_362_\ [+1(2.27e-05)]_26 49524 1.49e-07 49_[+1(2.82e-08)]_227_\ [+3(6.26e-05)]_50_[+3(8.85e-07)]_126 10319 1.42e-06 69_[+3(8.78e-05)]_5_[+2(9.34e-05)]_\ 156_[+1(1.18e-05)]_56_[+2(6.33e-08)]_140 33839 7.29e-06 74_[+1(1.66e-05)]_4_[+2(5.12e-07)]_\ 147_[+3(4.80e-05)]_222 7639 2.42e-03 62_[+1(2.27e-06)]_422 11230 2.07e-03 438_[+3(2.84e-07)]_46 44938 8.51e-10 107_[+2(4.28e-09)]_69_\ [+1(3.33e-08)]_287 11799 8.72e-02 500 7335 4.56e-08 103_[+3(3.18e-06)]_202_\ [+2(2.02e-07)]_32_[+3(9.52e-05)]_87_[+1(2.27e-06)]_7 8270 4.66e-01 500 45697 2.17e-04 404_[+2(1.11e-07)]_33_\ [+3(9.52e-05)]_26 12366 3.12e-03 206_[+1(6.76e-07)]_278 36139 1.29e-01 441_[+3(9.52e-05)]_43 46285 1.87e-04 13_[+3(1.33e-05)]_106_\ [+2(1.08e-06)]_344 31763 1.22e-02 93_[+1(7.63e-06)]_391 44274 5.46e-04 228_[+1(1.18e-05)]_229_\ [+3(1.06e-05)]_11 43283 3.80e-05 288_[+2(2.04e-08)]_1_[+3(8.78e-05)]_\ 174 49668 8.57e-04 5_[+3(2.47e-05)]_164_[+1(1.36e-05)]_\ 299 47477 4.83e-04 99_[+1(1.97e-07)]_385 48058 1.09e-05 437_[+3(1.03e-06)]_13_\ [+1(9.67e-07)]_18 38166 1.16e-05 217_[+3(1.82e-05)]_62_\ [+2(1.01e-07)]_184 40347 3.01e-09 131_[+1(5.29e-07)]_129_\ [+3(4.38e-05)]_58_[+3(4.13e-06)]_56_[+2(3.48e-08)]_57 39648 1.74e-04 154_[+1(6.52e-06)]_184_\ [+3(3.65e-05)]_97_[+3(5.29e-06)]_17 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************