******************************************************************************** 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/177/177.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31683 1.0000 500 8987 1.0000 500 42982 1.0000 500 9210 1.0000 500 20757 1.0000 500 36347 1.0000 500 36362 1.0000 500 13265 1.0000 500 7626 1.0000 500 14808 1.0000 500 15068 1.0000 500 22819 1.0000 500 33017 1.0000 500 43737 1.0000 500 49437 1.0000 500 15980 1.0000 500 16322 1.0000 500 52655 1.0000 500 16545 1.0000 500 31109 1.0000 500 50411 1.0000 500 10640 1.0000 500 44529 1.0000 500 51811 1.0000 500 45238 1.0000 500 45845 1.0000 500 12807 1.0000 500 49154 1.0000 500 43209 1.0000 500 38227 1.0000 500 40877 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/177/177.seqs.fa -oc motifs/177 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.238 C 0.260 G 0.240 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.238 C 0.260 G 0.240 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 21 llr = 206 E-value = 1.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 26621::a9:3: pos.-specific C 84:3::4::31: probability G ::35:16::6:: matrix T ::::99::::6a bits 2.1 * 1.9 * 1.7 * * 1.4 ** ** * Relative 1.2 * ** ** * Entropy 1.0 * ***** * (14.2 bits) 0.8 *** ****** * 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAAGTTGAAGTT consensus CGC C CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45845 190 1.69e-07 GTCCTTCGAT CAACTTGAAGTT GTAGCATACT 43737 154 3.89e-07 GCGGATACGT CAAGTTGAACTT GTACCGATCT 13265 169 3.89e-07 CGATCCGGGA CAAGTTGAACTT TTCCTACCAG 20757 309 1.04e-06 ACGTTCACTC CCGGTTGAAGTT GCGACAGATC 31683 128 1.04e-06 AGATTCCGTG CCGGTTGAAGTT CCCCCCAGCC 38227 391 1.85e-06 ACTTCGACTT CAACTTCAAGAT CCGACCGCTC 43209 188 5.19e-06 TTGCGGCAAG CAACTTGAAGCT GAAGCTCGGT 16322 103 6.25e-06 TACGTCAGTC ACGGTTGAAGTT GCAAATTGGA 40877 373 7.51e-06 GACAGACAGA CCGCTTCAACTT GCCAATCTTT 49154 266 9.00e-06 TCTACGCGCC CAAGTTGAAGTG TTGAAAGCAA 7626 76 1.00e-05 AAAGATAAGA CAAATGCAAGTT CTCTTCGTCA 45238 321 1.54e-05 ACAGGCTCGC CAACTTCAATTT GGGCGTAAAT 15068 81 2.14e-05 TTTCTTCCGT CAAAATGAAGAT TTCCCTGCTT 9210 51 2.51e-05 AGATTCCATC AACGTTGAAGTT ACTTTACAAA 36347 78 2.71e-05 CCCCCGCAAA CGACTTCAACTT GGGGTCCGGA 50411 30 3.37e-05 CCACGCTATA CAGGTTGATGAT TGTGATTGGT 22819 471 3.85e-05 CGTCCCCGTC CCACTGCAACAT TTCGGCTCCG 44529 239 4.70e-05 AACACTGGAA CCAATTCACGTT TGTGACGTCA 12807 12 5.30e-05 TACGTGTTCC ACGGTGGAAGAT CCTTGCAATC 36362 240 5.30e-05 TATGTTTCCG AAGGTTCAACCT GGAAGACGGA 33017 58 7.16e-05 GTTTCATCCT CCAAATCAACAT GGATGATGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45845 1.7e-07 189_[+1]_299 43737 3.9e-07 153_[+1]_335 13265 3.9e-07 168_[+1]_320 20757 1e-06 308_[+1]_180 31683 1e-06 127_[+1]_361 38227 1.9e-06 390_[+1]_98 43209 5.2e-06 187_[+1]_301 16322 6.3e-06 102_[+1]_386 40877 7.5e-06 372_[+1]_116 49154 9e-06 265_[+1]_223 7626 1e-05 75_[+1]_413 45238 1.5e-05 320_[+1]_168 15068 2.1e-05 80_[+1]_408 9210 2.5e-05 50_[+1]_438 36347 2.7e-05 77_[+1]_411 50411 3.4e-05 29_[+1]_459 22819 3.8e-05 470_[+1]_18 44529 4.7e-05 238_[+1]_250 12807 5.3e-05 11_[+1]_477 36362 5.3e-05 239_[+1]_249 33017 7.2e-05 57_[+1]_431 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=21 45845 ( 190) CAACTTGAAGTT 1 43737 ( 154) CAAGTTGAACTT 1 13265 ( 169) CAAGTTGAACTT 1 20757 ( 309) CCGGTTGAAGTT 1 31683 ( 128) CCGGTTGAAGTT 1 38227 ( 391) CAACTTCAAGAT 1 43209 ( 188) CAACTTGAAGCT 1 16322 ( 103) ACGGTTGAAGTT 1 40877 ( 373) CCGCTTCAACTT 1 49154 ( 266) CAAGTTGAAGTG 1 7626 ( 76) CAAATGCAAGTT 1 45238 ( 321) CAACTTCAATTT 1 15068 ( 81) CAAAATGAAGAT 1 9210 ( 51) AACGTTGAAGTT 1 36347 ( 78) CGACTTCAACTT 1 50411 ( 30) CAGGTTGATGAT 1 22819 ( 471) CCACTGCAACAT 1 44529 ( 239) CCAATTCACGTT 1 12807 ( 12) ACGGTGGAAGAT 1 36362 ( 240) AAGGTTCAACCT 1 33017 ( 58) CCAAATCAACAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 15159 bayes= 10.4809 E= 1.9e-002 -32 164 -1104 -1104 126 55 -233 -1104 138 -245 47 -1104 -32 36 99 -1104 -132 -1104 -1104 179 -1104 -1104 -75 171 -1104 72 125 -1104 207 -1104 -1104 -1104 193 -245 -1104 -245 -1104 36 137 -245 26 -145 -1104 124 -1104 -1104 -233 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 21 E= 1.9e-002 0.190476 0.809524 0.000000 0.000000 0.571429 0.380952 0.047619 0.000000 0.619048 0.047619 0.333333 0.000000 0.190476 0.333333 0.476190 0.000000 0.095238 0.000000 0.000000 0.904762 0.000000 0.000000 0.142857 0.857143 0.000000 0.428571 0.571429 0.000000 1.000000 0.000000 0.000000 0.000000 0.904762 0.047619 0.000000 0.047619 0.000000 0.333333 0.619048 0.047619 0.285714 0.095238 0.000000 0.619048 0.000000 0.000000 0.047619 0.952381 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC][AG][GC]TT[GC]AA[GC][TA]T -------------------------------------------------------------------------------- Time 7.59 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 20 llr = 216 E-value = 9.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 7:a:3:819:2:7351 pos.-specific C :8:82727:5193427 probability G :2::2311:5:111:: matrix T 4::33::21:8::333 bits 2.1 * 1.9 * 1.7 * * 1.4 * * * Relative 1.2 ** * * Entropy 1.0 **** ** ***** (15.6 bits) 0.8 **** ** ***** 0.6 **** ******** ** 0.4 **** ******** ** 0.2 **** *********** 0.0 ---------------- Multilevel ACACACACACTCACAC consensus TG TTGCT GA CATT sequence C TC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 15068 259 1.33e-09 ATTCTCACAC ACACACACACTCACAC ACACACACGT 36362 344 6.30e-08 CTTTGTGTAT ACACGCACAGTCATAT CCTTGTATTT 33017 336 2.36e-07 AACACGAGCA ACATCGACAGTCAAAC GGGTTGCCCC 9210 158 4.13e-07 CTCGTCCTTC TCACTCACAGTCAACT GGTCTTTGTT 52655 59 5.40e-07 GTTCACAGTC ACACTCACTGTCACTC CAGAGTCAAC 38227 157 6.97e-07 TGGTACCTTT TCACTCATAGTCCCAC ATTTTATTCG 36347 157 8.89e-07 TCTCTCCCTA TCACACATACACACAC ATCACGGTCC 16322 80 1.77e-06 GACTCGTCAA ACACGGACTCTCATAC GTCAGTCACG 50411 269 2.96e-06 ATCGATACCG ACACGGACACTGATTC TACGTTCGTG 49154 411 4.35e-06 CAAGCCAAGG AGACCCCCAGACAAAC CAAGCGCTCC 15980 409 4.35e-06 TATCAAGACC TCACCCACACCCAATC GTCATTTATG 20757 253 4.35e-06 TAGAGGTCCC ACACCCAAACACACCC GGACACGTGA 45238 361 7.39e-06 CGATGAAACC AGATTCACAGTCAGTT TCAAAACTGT 44529 25 1.02e-05 GCCGAAGCCA TCACAGACAGTCCTCA GGATTCCAAA 22819 413 1.29e-05 ATGCCGTCTC TCACACCTACTCCTCC TTTCTCTACT 45845 167 1.61e-05 TTCACGAGTG TGATTCACAGTCCGTC CTTCGATCAA 43209 155 2.42e-05 ATTGTCTGAG ACACACAAACACGAAT CACTTTGTTG 7626 252 2.93e-05 ACTTCAACTC ACATTCCGACTCAAAA AGGGAACGAA 31109 167 3.51e-05 CATACATTAT ACATAGGTAGTCACTT ACAACTAATA 8987 460 3.94e-05 GAATTTGGCC AGACGGCCACTGCCAC GACGTTTGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15068 1.3e-09 258_[+2]_226 36362 6.3e-08 343_[+2]_141 33017 2.4e-07 335_[+2]_149 9210 4.1e-07 157_[+2]_327 52655 5.4e-07 58_[+2]_426 38227 7e-07 156_[+2]_328 36347 8.9e-07 156_[+2]_328 16322 1.8e-06 79_[+2]_405 50411 3e-06 268_[+2]_216 49154 4.4e-06 410_[+2]_74 15980 4.4e-06 408_[+2]_76 20757 4.4e-06 252_[+2]_232 45238 7.4e-06 360_[+2]_124 44529 1e-05 24_[+2]_460 22819 1.3e-05 412_[+2]_72 45845 1.6e-05 166_[+2]_318 43209 2.4e-05 154_[+2]_330 7626 2.9e-05 251_[+2]_233 31109 3.5e-05 166_[+2]_318 8987 3.9e-05 459_[+2]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=20 15068 ( 259) ACACACACACTCACAC 1 36362 ( 344) ACACGCACAGTCATAT 1 33017 ( 336) ACATCGACAGTCAAAC 1 9210 ( 158) TCACTCACAGTCAACT 1 52655 ( 59) ACACTCACTGTCACTC 1 38227 ( 157) TCACTCATAGTCCCAC 1 36347 ( 157) TCACACATACACACAC 1 16322 ( 80) ACACGGACTCTCATAC 1 50411 ( 269) ACACGGACACTGATTC 1 49154 ( 411) AGACCCCCAGACAAAC 1 15980 ( 409) TCACCCACACCCAATC 1 20757 ( 253) ACACCCAAACACACCC 1 45238 ( 361) AGATTCACAGTCAGTT 1 44529 ( 25) TCACAGACAGTCCTCA 1 22819 ( 413) TCACACCTACTCCTCC 1 45845 ( 167) TGATTCACAGTCCGTC 1 43209 ( 155) ACACACAAACACGAAT 1 7626 ( 252) ACATTCCGACTCAAAA 1 31109 ( 167) ACATAGGTAGTCACTT 1 8987 ( 460) AGACGGCCACTGCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15035 bayes= 9.80403 E= 9.9e-002 145 -1097 -1097 42 -1097 162 -26 -1097 207 -1097 -1097 -1097 -1097 153 -1097 -6 33 -38 -26 20 -1097 143 32 -1097 166 -38 -226 -1097 -125 132 -226 -39 192 -1097 -1097 -138 -1097 94 106 -1097 -25 -238 -1097 152 -1097 179 -126 -1097 156 -6 -226 -1097 33 43 -126 -6 107 -38 -1097 20 -125 132 -1097 -6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 9.9e-002 0.650000 0.000000 0.000000 0.350000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.300000 0.200000 0.200000 0.300000 0.000000 0.700000 0.300000 0.000000 0.750000 0.200000 0.050000 0.000000 0.100000 0.650000 0.050000 0.200000 0.900000 0.000000 0.000000 0.100000 0.000000 0.500000 0.500000 0.000000 0.200000 0.050000 0.000000 0.750000 0.000000 0.900000 0.100000 0.000000 0.700000 0.250000 0.050000 0.000000 0.300000 0.350000 0.100000 0.250000 0.500000 0.200000 0.000000 0.300000 0.100000 0.650000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][CG]A[CT][ATCG][CG][AC][CT]A[CG][TA]C[AC][CAT][ATC][CT] -------------------------------------------------------------------------------- Time 15.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 31 llr = 272 E-value = 1.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 52:::::::1:21:1: pos.-specific C 212:46::31311133 probability G 21:95:1242:73216 matrix T 26811498367:6751 bits 2.1 1.9 1.7 * 1.4 * * Relative 1.2 ** ** Entropy 1.0 ** ** * (12.7 bits) 0.8 *** ** ** * 0.6 ****** ** * * 0.4 ******* ******* 0.2 **************** 0.0 ---------------- Multilevel ATTGGCTTGTTGTTTG consensus CT C C G CC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8987 207 2.77e-10 CAAACGGCAT ATTGGCTTGTTGTTTG CTACGTTACC 43737 183 1.01e-06 TCTTGCCCGC GTTGGCTTCGTGTTGG GAACGTGTAT 12807 81 1.33e-06 ACGGACCGTC ATCGGCTTGTCGTTCC TCCTTCCTCT 44529 103 1.52e-06 CTAAAGGTAT AATGGTTGGTTGGTTG GGTTGTTGGT 42982 480 3.29e-06 CGGCAGGACC TTTGGCTGGTTGCTTG TGCTT 31109 359 4.73e-06 CGGGGATCGG ATTGGTGTTTTGTGTG TTCGTTAGAG 9210 218 4.73e-06 TCGGCGTCTC ATTGGCTTTCTATTCC TGTTGAAAGA 38227 90 6.71e-06 CGCATTGCGC TCTGCCTTTTTGGTCG ACGCATAGTG 45845 391 6.71e-06 CGCCGATCTC CTTGCTTTCTCATTCG ATTCTTCTTT 22819 142 7.51e-06 GGCTCCTCAT TGTGGTTGCTTGTTTG GACCTACGGC 31683 14 7.51e-06 TATGTCGTAA GATGGCTTCTTCTTTC TAACCAGATC 50411 117 1.44e-05 CCTTCCTTCC TTTGTTTGTTTGTTTG TTTGCGATAT 7626 315 1.59e-05 TCGCTGCCTA ATTGGCTTGGCCTTAG CCCTATATCA 36347 456 1.95e-05 CACGGAATGA CTTGCATGTTTGTTTG ATTTTGGTTA 20757 57 1.95e-05 TGGTGTGCCA ATTGGCTTACTATTCG ATTCACAGTC 13265 140 2.38e-05 TTGGGTGAAC GATGCCTTGGCGTTCC CCCCGATCCG 36362 179 2.38e-05 AACTGTGCTG TCCGGTTTCGTGTTTG TGTCGTAGCT 51811 138 2.89e-05 AGTTTCCCAA ATTGCGTTGTCGATTG ACAGTGAACA 14808 149 2.89e-05 TCCACAGGTC GTTGCCTTCCTCGTCG TTTATTACCA 40877 172 4.20e-05 CACAATCAGC GTTGGTTTCTTGGTAT ACGTCAACCA 49437 432 4.59e-05 CTGCTTCTCG AGTGTTTTGTTGTGTC TATTCCCACA 45238 210 5.99e-05 TGTTGACGGT CATGCTTTTTCGGCTG CTATGCTACT 15980 443 8.40e-05 TGGTTCGTCT CCTGCCTTTTCAGTTC ACACGCGACG 15068 217 8.40e-05 GACCGGAAGA ATCGCCGTGTCGTCTG CACCTGTAGG 10640 402 9.12e-05 TCATGAATTC ATTGCTTTCGTGCGGC TATAGGACAA 33017 248 9.89e-05 TTCTCACAAA AGTGGCTTCTTATCGC ATCCGTGTTT 52655 332 1.83e-04 GTGTATGGAA ATCCCTTTCGTGTGTG CTCACTGTAG 16322 372 2.62e-04 AGCACCGTTC AACTGCTTGTTGATCC CGAAAATGAT 49154 387 2.81e-04 GTCCGACTGA ATTGGCTTTCTCCTCA AGCCAAGGAG 43209 370 3.22e-04 TCAACCAGTC CTTTGCTTTATGGTTT ATAGGCTTTT 16545 195 3.68e-04 CCCGGTGCGA CTCGCCTTGACGGGGG AAATGAGCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8987 2.8e-10 206_[+3]_278 43737 1e-06 182_[+3]_302 12807 1.3e-06 80_[+3]_404 44529 1.5e-06 102_[+3]_382 42982 3.3e-06 479_[+3]_5 31109 4.7e-06 358_[+3]_126 9210 4.7e-06 217_[+3]_267 38227 6.7e-06 89_[+3]_395 45845 6.7e-06 390_[+3]_94 22819 7.5e-06 141_[+3]_343 31683 7.5e-06 13_[+3]_471 50411 1.4e-05 116_[+3]_368 7626 1.6e-05 314_[+3]_170 36347 2e-05 455_[+3]_29 20757 2e-05 56_[+3]_428 13265 2.4e-05 139_[+3]_345 36362 2.4e-05 178_[+3]_306 51811 2.9e-05 137_[+3]_347 14808 2.9e-05 148_[+3]_336 40877 4.2e-05 171_[+3]_313 49437 4.6e-05 431_[+3]_53 45238 6e-05 209_[+3]_275 15980 8.4e-05 442_[+3]_42 15068 8.4e-05 216_[+3]_268 10640 9.1e-05 401_[+3]_83 33017 9.9e-05 247_[+3]_237 52655 0.00018 331_[+3]_153 16322 0.00026 371_[+3]_113 49154 0.00028 386_[+3]_98 43209 0.00032 369_[+3]_115 16545 0.00037 194_[+3]_290 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=31 8987 ( 207) ATTGGCTTGTTGTTTG 1 43737 ( 183) GTTGGCTTCGTGTTGG 1 12807 ( 81) ATCGGCTTGTCGTTCC 1 44529 ( 103) AATGGTTGGTTGGTTG 1 42982 ( 480) TTTGGCTGGTTGCTTG 1 31109 ( 359) ATTGGTGTTTTGTGTG 1 9210 ( 218) ATTGGCTTTCTATTCC 1 38227 ( 90) TCTGCCTTTTTGGTCG 1 45845 ( 391) CTTGCTTTCTCATTCG 1 22819 ( 142) TGTGGTTGCTTGTTTG 1 31683 ( 14) GATGGCTTCTTCTTTC 1 50411 ( 117) TTTGTTTGTTTGTTTG 1 7626 ( 315) ATTGGCTTGGCCTTAG 1 36347 ( 456) CTTGCATGTTTGTTTG 1 20757 ( 57) ATTGGCTTACTATTCG 1 13265 ( 140) GATGCCTTGGCGTTCC 1 36362 ( 179) TCCGGTTTCGTGTTTG 1 51811 ( 138) ATTGCGTTGTCGATTG 1 14808 ( 149) GTTGCCTTCCTCGTCG 1 40877 ( 172) GTTGGTTTCTTGGTAT 1 49437 ( 432) AGTGTTTTGTTGTGTC 1 45238 ( 210) CATGCTTTTTCGGCTG 1 15980 ( 443) CCTGCCTTTTCAGTTC 1 15068 ( 217) ATCGCCGTGTCGTCTG 1 10640 ( 402) ATTGCTTTCGTGCGGC 1 33017 ( 248) AGTGGCTTCTTATCGC 1 52655 ( 332) ATCCCTTTCGTGTGTG 1 16322 ( 372) AACTGCTTGTTGATCC 1 49154 ( 387) ATTGGCTTTCTCCTCA 1 43209 ( 370) CTTTGCTTTATGGTTT 1 16545 ( 195) CTCGCCTTGACGGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15035 bayes= 8.91886 E= 1.0e+000 102 -43 -57 -70 -56 -143 -131 130 -1160 -43 -1160 163 -1160 -301 191 -202 -1160 57 119 -202 -288 116 -289 44 -1160 -1160 -190 184 -1160 -1160 -57 168 -288 31 56 15 -188 -101 -31 123 -1160 16 -1160 144 -56 -101 156 -1160 -188 -143 10 115 -1160 -143 -57 150 -188 16 -90 98 -288 16 135 -202 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 31 E= 1.0e+000 0.483871 0.193548 0.161290 0.161290 0.161290 0.096774 0.096774 0.645161 0.000000 0.193548 0.000000 0.806452 0.000000 0.032258 0.903226 0.064516 0.000000 0.387097 0.548387 0.064516 0.032258 0.580645 0.032258 0.354839 0.000000 0.000000 0.064516 0.935484 0.000000 0.000000 0.161290 0.838710 0.032258 0.322581 0.354839 0.290323 0.064516 0.129032 0.193548 0.612903 0.000000 0.290323 0.000000 0.709677 0.161290 0.129032 0.709677 0.000000 0.064516 0.096774 0.258065 0.580645 0.000000 0.096774 0.161290 0.741935 0.064516 0.290323 0.129032 0.516129 0.032258 0.290323 0.612903 0.064516 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- ATTG[GC][CT]TT[GCT]T[TC]G[TG]T[TC][GC] -------------------------------------------------------------------------------- Time 22.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31683 9.60e-05 13_[+3(7.51e-06)]_98_[+1(1.04e-06)]_\ 146_[+1(3.42e-06)]_88_[+1(4.22e-06)]_103 8987 9.94e-08 206_[+3(2.77e-10)]_237_\ [+2(3.94e-05)]_25 42982 8.09e-03 479_[+3(3.29e-06)]_5 9210 1.12e-06 50_[+1(2.51e-05)]_95_[+2(4.13e-07)]_\ 44_[+3(4.73e-06)]_267 20757 1.91e-06 56_[+3(1.95e-05)]_180_\ [+2(4.35e-06)]_40_[+1(1.04e-06)]_98_[+1(7.60e-05)]_70 36347 8.46e-06 77_[+1(2.71e-05)]_67_[+2(8.89e-07)]_\ 283_[+3(1.95e-05)]_29 36362 1.72e-06 178_[+3(2.38e-05)]_45_\ [+1(5.30e-05)]_92_[+2(6.30e-08)]_141 13265 1.94e-04 139_[+3(2.38e-05)]_13_\ [+1(3.89e-07)]_320 7626 6.36e-05 75_[+1(1.00e-05)]_164_\ [+2(2.93e-05)]_47_[+3(1.59e-05)]_170 14808 1.03e-01 148_[+3(2.89e-05)]_336 15068 7.09e-08 80_[+1(2.14e-05)]_124_\ [+3(8.40e-05)]_26_[+2(1.33e-09)]_226 22819 5.21e-05 141_[+3(7.51e-06)]_255_\ [+2(1.29e-05)]_42_[+1(3.85e-05)]_18 33017 2.52e-05 57_[+1(7.16e-05)]_178_\ [+3(9.89e-05)]_72_[+2(2.36e-07)]_149 43737 9.94e-06 153_[+1(3.89e-07)]_17_\ [+3(1.01e-06)]_302 49437 6.88e-02 431_[+3(4.59e-05)]_53 15980 3.47e-03 408_[+2(4.35e-06)]_18_\ [+3(8.40e-05)]_42 16322 4.00e-05 79_[+2(1.77e-06)]_7_[+1(6.25e-06)]_\ 386 52655 1.35e-03 58_[+2(5.40e-07)]_426 16545 5.59e-01 500 31109 1.98e-03 166_[+2(3.51e-05)]_176_\ [+3(4.73e-06)]_126 50411 2.26e-05 29_[+1(3.37e-05)]_75_[+3(1.44e-05)]_\ 136_[+2(2.96e-06)]_216 10640 2.76e-01 401_[+3(9.12e-05)]_83 44529 1.24e-05 24_[+2(1.02e-05)]_62_[+3(1.52e-06)]_\ 120_[+1(4.70e-05)]_250 51811 8.96e-02 137_[+3(2.89e-05)]_347 45238 8.75e-05 209_[+3(5.99e-05)]_95_\ [+1(1.54e-05)]_28_[+2(7.39e-06)]_124 45845 4.61e-07 166_[+2(1.61e-05)]_7_[+1(1.69e-07)]_\ 189_[+3(6.71e-06)]_94 12807 1.18e-03 11_[+1(5.30e-05)]_57_[+3(1.33e-06)]_\ 404 49154 1.27e-04 265_[+1(9.00e-06)]_133_\ [+2(4.35e-06)]_74 43209 3.84e-04 154_[+2(2.42e-05)]_17_\ [+1(5.19e-06)]_301 38227 2.36e-07 89_[+3(6.71e-06)]_51_[+2(6.97e-07)]_\ 218_[+1(1.85e-06)]_98 40877 1.94e-03 171_[+3(4.20e-05)]_185_\ [+1(7.51e-06)]_116 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************