******************************************************************************** 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/407/407.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9252 1.0000 500 31529 1.0000 500 31684 1.0000 500 6927 1.0000 500 42799 1.0000 500 42972 1.0000 500 46390 1.0000 500 46648 1.0000 500 37254 1.0000 500 38390 1.0000 500 48037 1.0000 500 43402 1.0000 500 43539 1.0000 500 41268 1.0000 500 44363 1.0000 500 44501 1.0000 500 10799 1.0000 500 11259 1.0000 500 45111 1.0000 500 45216 1.0000 500 35054 1.0000 500 35296 1.0000 500 45698 1.0000 500 46135 1.0000 500 46214 1.0000 500 46264 1.0000 500 42698 1.0000 500 31874 1.0000 500 31876 1.0000 500 46895 1.0000 500 39506 1.0000 500 34899 1.0000 500 36402 1.0000 500 44830 1.0000 500 36434 1.0000 500 36514 1.0000 500 37648 1.0000 500 43894 1.0000 500 33005 1.0000 500 45822 1.0000 500 34528 1.0000 500 37029 1.0000 500 47034 1.0000 500 34230 1.0000 500 33881 1.0000 500 35182 1.0000 500 45981 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/407/407.seqs.fa -oc motifs/407 -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= 47 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= 23500 N= 47 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.234 G 0.221 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.234 G 0.221 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 21 llr = 233 E-value = 7.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::7:6:::44621515 pos.-specific C ::1a::::25:31441 probability G ::2::7::31:11:2: matrix T aa::43aa::446:34 bits 2.2 * 2.0 * * ** 1.7 * * ** 1.5 ** * ** Relative 1.3 ** * *** Entropy 1.1 ** * *** (16.0 bits) 0.9 ******** * 0.7 ******** ** * 0.4 *********** * * 0.2 *********** **** 0.0 ---------------- Multilevel TTACAGTTACATTACA consensus TT GATC CTT sequence C A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 47034 417 8.94e-08 CTGGTAGCGC TTACAGTTACTTTATT TGTAAACCAG 42799 408 8.94e-08 AGGGATGGGC TTACATTTACATTACA TGTACTTTAC 46390 133 2.39e-07 GGTTTTACGA TTACTGTTCCACTCCT CCTGGTCACT 46214 279 4.03e-07 TGCGTGGAGC TTACAGTTAGACTCCT TACGCGACAG 44830 281 6.63e-07 GGATCGTATT TTACAGTTACAACATA GTCAATCCAT 44501 345 8.98e-07 GTCTCACAAT TTACTGTTGCATGAGT TGTACGCGAT 44363 366 1.20e-06 GAAATTGGTT TTACTGTTACATTCAT GGAATTTATC 33881 440 2.46e-06 CCGTCTCTGC TTACAGTTCATTGCTA TTCCTGATCT 35054 393 4.12e-06 CGAAAAAGCA TTACATTTCAACAACA ATTTCGCATA 34899 299 4.98e-06 CTCTCTTTTG TTACTGTTGATACAGT TAGTTACCTG 34528 149 5.44e-06 GCTACTTTCT TTACAGTTGATGTCCC CAATTTCAAC 31684 442 5.94e-06 TCTAAACATC TTGCAGTTACAGACCA CCTCTCGTAT 34230 480 7.01e-06 TACAAATGAG TTGCAGTTGATACAGA ACAAC 38390 441 7.01e-06 ACAACACCCG TTCCAGTTCCACGAGA ATCAGATTAG 43894 218 7.59e-06 ACACGCAGAC TTGCTTTTGAAATCTA CGGAACGGTC 46264 309 8.85e-06 CGACTTACTG TTACTGTTAGATTTCT GCTACATTTA 31529 314 8.85e-06 TTAGTCAAAA TTCCATTTACTATATA CCGTTAAAAC 45822 357 1.02e-05 GCCTCTTTCT TTGCTGTTGGATTCAA GCTTCTGGCT 46895 285 1.09e-05 GTATGAACTT TAACATTTGCTTTACA ACAAGTAAAG 46648 482 1.25e-05 GCAAGCTCGC TTACAGTTAAACAGGT AGG 36402 60 1.42e-05 GCGCTATATT TTACTTTTCATCTATC CCCTCGGTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47034 8.9e-08 416_[+1]_68 42799 8.9e-08 407_[+1]_77 46390 2.4e-07 132_[+1]_352 46214 4e-07 278_[+1]_206 44830 6.6e-07 280_[+1]_204 44501 9e-07 344_[+1]_140 44363 1.2e-06 365_[+1]_119 33881 2.5e-06 439_[+1]_45 35054 4.1e-06 392_[+1]_92 34899 5e-06 298_[+1]_186 34528 5.4e-06 148_[+1]_336 31684 5.9e-06 441_[+1]_43 34230 7e-06 479_[+1]_5 38390 7e-06 440_[+1]_44 43894 7.6e-06 217_[+1]_267 46264 8.8e-06 308_[+1]_176 31529 8.8e-06 313_[+1]_171 45822 1e-05 356_[+1]_128 46895 1.1e-05 284_[+1]_200 46648 1.3e-05 481_[+1]_3 36402 1.4e-05 59_[+1]_425 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=21 47034 ( 417) TTACAGTTACTTTATT 1 42799 ( 408) TTACATTTACATTACA 1 46390 ( 133) TTACTGTTCCACTCCT 1 46214 ( 279) TTACAGTTAGACTCCT 1 44830 ( 281) TTACAGTTACAACATA 1 44501 ( 345) TTACTGTTGCATGAGT 1 44363 ( 366) TTACTGTTACATTCAT 1 33881 ( 440) TTACAGTTCATTGCTA 1 35054 ( 393) TTACATTTCAACAACA 1 34899 ( 299) TTACTGTTGATACAGT 1 34528 ( 149) TTACAGTTGATGTCCC 1 31684 ( 442) TTGCAGTTACAGACCA 1 34230 ( 480) TTGCAGTTGATACAGA 1 38390 ( 441) TTCCAGTTCCACGAGA 1 43894 ( 218) TTGCTTTTGAAATCTA 1 46264 ( 309) TTACTGTTAGATTTCT 1 31529 ( 314) TTCCATTTACTATATA 1 45822 ( 357) TTGCTGTTGGATTCAA 1 46895 ( 285) TAACATTTGCTTTACA 1 46648 ( 482) TTACAGTTAAACAGGT 1 36402 ( 60) TTACTTTTCATCTATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 11.0698 E= 7.5e-002 -1104 -1104 -1104 190 -253 -1104 -1104 183 137 -130 -22 -1104 -1104 210 -1104 -1104 116 -1104 -1104 51 -1104 -1104 169 9 -1104 -1104 -1104 190 -1104 -1104 -1104 190 63 3 59 -1104 46 103 -63 -1104 116 -1104 -1104 51 -22 29 -122 51 -95 -71 -63 109 92 70 -221 -249 -154 70 10 9 92 -130 -1104 51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 21 E= 7.5e-002 0.000000 0.000000 0.000000 1.000000 0.047619 0.000000 0.000000 0.952381 0.714286 0.095238 0.190476 0.000000 0.000000 1.000000 0.000000 0.000000 0.619048 0.000000 0.000000 0.380952 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.428571 0.238095 0.333333 0.000000 0.380952 0.476190 0.142857 0.000000 0.619048 0.000000 0.000000 0.380952 0.238095 0.285714 0.095238 0.380952 0.142857 0.142857 0.142857 0.571429 0.523810 0.380952 0.047619 0.047619 0.095238 0.380952 0.238095 0.285714 0.523810 0.095238 0.000000 0.380952 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTAC[AT][GT]TT[AGC][CA][AT][TCA]T[AC][CTG][AT] -------------------------------------------------------------------------------- Time 17.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 7 llr = 129 E-value = 1.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1::1a7::769::41:::: pos.-specific C :3:7::::634:aa4:a1:a probability G 747:3:1:4::1:::1:9:: matrix T 31336:1a::::::17::a: bits 2.2 ** * * 2.0 * * ** * ** 1.7 * * ** * ** 1.5 * * ** **** Relative 1.3 * * * * *** **** Entropy 1.1 * ** * *** *** **** (26.6 bits) 0.9 * ** * ******* ***** 0.7 * ************ ***** 0.4 * ****************** 0.2 ******************** 0.0 -------------------- Multilevel GGGCTAATCAAACCATCGTC consensus TCTTG GCC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 37029 311 7.71e-13 CAGTGCGGGG GGGCTAATCAAACCCTCGTC AGTCCCCGAG 39506 298 7.71e-13 TAGTACGGGG GGGCTAATCAAACCCTCGTC AGTCCCCGAG 46135 186 1.89e-09 CGGTGCGCTT GGTCTAATGCCACCCGCGTC CCAAAACCCA 38390 469 3.47e-09 CAGATTAGCT TTTCGAATCACACCATCGTC GTACCTTGGA 10799 56 1.35e-08 AAATTGAGCA GAGCAAGTCACACCAACGTC CGAGATCTTC 47034 315 1.41e-08 ACCTATTTGC GCGTGAATGCAACCTTCCTC ATGCAAACAA 46648 342 1.56e-08 TGCTGCTGTA TCGTTATTGAAGCCATCGTC ACCGGGTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37029 7.7e-13 310_[+2]_170 39506 7.7e-13 297_[+2]_183 46135 1.9e-09 185_[+2]_295 38390 3.5e-09 468_[+2]_12 10799 1.3e-08 55_[+2]_425 47034 1.4e-08 314_[+2]_166 46648 1.6e-08 341_[+2]_139 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=7 37029 ( 311) GGGCTAATCAAACCCTCGTC 1 39506 ( 298) GGGCTAATCAAACCCTCGTC 1 46135 ( 186) GGTCTAATGCCACCCGCGTC 1 38390 ( 469) TTTCGAATCACACCATCGTC 1 10799 ( 56) GAGCAAGTCACACCAACGTC 1 47034 ( 315) GCGTGAATGCAACCTTCCTC 1 46648 ( 342) TCGTTATTGAAGCCATCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 22607 bayes= 11.5005 E= 1.3e+000 -945 -945 169 9 -95 29 95 -91 -945 -945 169 9 -945 161 -945 9 -95 -945 37 109 185 -945 -945 -945 137 -945 -63 -91 -945 -945 -945 190 -945 129 95 -945 137 29 -945 -945 105 87 -945 -945 163 -945 -63 -945 -945 209 -945 -945 -945 209 -945 -945 63 87 -945 -91 -95 -945 -63 141 -945 209 -945 -945 -945 -71 195 -945 -945 -945 -945 190 -945 209 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7 E= 1.3e+000 0.000000 0.000000 0.714286 0.285714 0.142857 0.285714 0.428571 0.142857 0.000000 0.000000 0.714286 0.285714 0.000000 0.714286 0.000000 0.285714 0.142857 0.000000 0.285714 0.571429 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.142857 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.428571 0.000000 0.714286 0.285714 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.428571 0.000000 0.142857 0.142857 0.000000 0.142857 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][GC][GT][CT][TG]AAT[CG][AC][AC]ACC[AC]TCGTC -------------------------------------------------------------------------------- Time 35.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 27 llr = 291 E-value = 3.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3634978472:16a7176632 pos.-specific C 1431:3:3123:3::533312 probability G 6:231:2::3691:13:116: matrix T ::22:::2331:::2:::::5 bits 2.2 2.0 * 1.7 * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 *** * * (15.6 bits) 0.9 * *** * * * 0.7 ** *** * ***** ** * 0.4 ** *** * ********** 0.2 ** ****** *********** 0.0 --------------------- Multilevel GAAAAAAAAGGGAAACAAAGT consensus ACCG C CTTC C GCCCAA sequence T A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45822 385 1.83e-09 TTCTGGCTGA GAATAAACATGGAAACAAAAT TAGTCGAGTC 33005 420 6.04e-08 ATTGTCGGAT GCTGAAAAACGGCAAAAAAGT ACTATCAAAC 45981 41 1.09e-07 GAAGTATACC GACGAAATTGCGAATCAAAGT ACGATTCGTA 42972 267 2.48e-07 ATGTCTTGTG GATGAAGAATCGAAACAAACT AGTAGCACGA 36434 386 4.12e-07 GCACAACGCG AAGAACAAAGGGAAACCAGGC AAATACATAC 42799 101 8.38e-07 GGCTACGGAG GAGAAAAAATAGCAAGAAAGA AAAGGAATGT 46895 405 1.05e-06 AGGTAAGCAC GAAAAAACACCGAAAAACGAT CCAACGTAGA 6927 73 1.31e-06 AGCACCAACA GCTAAAAATCCGCATGACAGT GAAGAGCTGT 43894 10 1.99e-06 GAGCAAGTA GACTACAGAAGGAAAGCAAAT ACCAATATAG 45216 169 1.99e-06 ACTATCATAA GCATAAACTAGGTAACCACGT CACAAATCGG 36402 198 2.43e-06 CAGTAAAACA ACGTAAACATGGAAAGACATT TGAAAAGGAT 31529 76 2.69e-06 TAGTGTTCGC TCCGAAACAGGGCAACAACAC CGATTGGTAT 46135 446 3.60e-06 GTAAGTGTAA AATAAAGCAACGAAGCAAAGA AACCACGACG 41268 15 4.34e-06 CCATATTCCA GAAAAAATCTGGGAAGCAAAT TTGGGTATGG 9252 138 4.34e-06 TCCGGAAGAA GAACAAGAAGTGCAACCCCGT TACACAATTC 34230 358 4.76e-06 GACATTCTGG ACAGAAACTTGGAATCAGCAT TCTGGTCAAA 45111 187 4.76e-06 TAACGGTACA AAAGGCAAAAGGAAAGCAAGA CTACTGTTCT 37254 140 5.21e-06 TCGACTTCGT GATGACATATTGAAATAAAGT TGATCGTTAT 31876 199 5.70e-06 CCAGGCAATA CCCAACAAACGGGAGCAAAGT GATTAGCAAT 33881 362 8.09e-06 AAATTCCTGT GCGAAAAAAGCAAAAGCGCGC ACAGGCTGCG 11259 116 1.33e-05 ACAGCGAGCT GCCTACGTTTGGAAACAATGA GAATGACAAC 35296 297 1.55e-05 GGATGAGTGC GAGTAAAATGGAAATAAACGC ACATAATTTC 47034 92 2.27e-05 CGCTTCCGTC CCACACACAACGAATCACAGC CCCACAGTCC 44830 98 2.44e-05 TCGATGAAAC GAAAAAGTTCTGCAACACCAA GGACTCTAAC 10799 271 2.44e-05 GTCGAGTCTT ACCAAAAAAAGGCAACGGACC CCGATTTGCG 39506 410 2.81e-05 AGTCCGCTAT AACAAAACAGCGAAGGACCCG AACCCATAAT 46214 300 2.81e-05 CTCCTTACGC GACAGAAACGGGAAAACCGGA TTTTTCGAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45822 1.8e-09 384_[+3]_95 33005 6e-08 419_[+3]_60 45981 1.1e-07 40_[+3]_439 42972 2.5e-07 266_[+3]_213 36434 4.1e-07 385_[+3]_94 42799 8.4e-07 100_[+3]_379 46895 1e-06 404_[+3]_75 6927 1.3e-06 72_[+3]_407 43894 2e-06 9_[+3]_470 45216 2e-06 168_[+3]_311 36402 2.4e-06 197_[+3]_282 31529 2.7e-06 75_[+3]_404 46135 3.6e-06 445_[+3]_34 41268 4.3e-06 14_[+3]_465 9252 4.3e-06 137_[+3]_342 34230 4.8e-06 357_[+3]_122 45111 4.8e-06 186_[+3]_293 37254 5.2e-06 139_[+3]_340 31876 5.7e-06 198_[+3]_281 33881 8.1e-06 361_[+3]_118 11259 1.3e-05 115_[+3]_364 35296 1.6e-05 296_[+3]_183 47034 2.3e-05 91_[+3]_388 44830 2.4e-05 97_[+3]_382 10799 2.4e-05 270_[+3]_209 39506 2.8e-05 409_[+3]_70 46214 2.8e-05 299_[+3]_180 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=27 45822 ( 385) GAATAAACATGGAAACAAAAT 1 33005 ( 420) GCTGAAAAACGGCAAAAAAGT 1 45981 ( 41) GACGAAATTGCGAATCAAAGT 1 42972 ( 267) GATGAAGAATCGAAACAAACT 1 36434 ( 386) AAGAACAAAGGGAAACCAGGC 1 42799 ( 101) GAGAAAAAATAGCAAGAAAGA 1 46895 ( 405) GAAAAAACACCGAAAAACGAT 1 6927 ( 73) GCTAAAAATCCGCATGACAGT 1 43894 ( 10) GACTACAGAAGGAAAGCAAAT 1 45216 ( 169) GCATAAACTAGGTAACCACGT 1 36402 ( 198) ACGTAAACATGGAAAGACATT 1 31529 ( 76) TCCGAAACAGGGCAACAACAC 1 46135 ( 446) AATAAAGCAACGAAGCAAAGA 1 41268 ( 15) GAAAAAATCTGGGAAGCAAAT 1 9252 ( 138) GAACAAGAAGTGCAACCCCGT 1 34230 ( 358) ACAGAAACTTGGAATCAGCAT 1 45111 ( 187) AAAGGCAAAAGGAAAGCAAGA 1 37254 ( 140) GATGACATATTGAAATAAAGT 1 31876 ( 199) CCCAACAAACGGGAGCAAAGT 1 33881 ( 362) GCGAAAAAAGCAAAAGCGCGC 1 11259 ( 116) GCCTACGTTTGGAAACAATGA 1 35296 ( 297) GAGTAAAATGGAAATAAACGC 1 47034 ( 92) CCACACACAACGAATCACAGC 1 44830 ( 98) GAAAAAGTTCTGCAACACCAA 1 10799 ( 271) ACCAAAAAAAGGCAACGGACC 1 39506 ( 410) AACAAAACAGCGAAGGACCCG 1 46214 ( 300) GACAGAAACGGGAAAACCGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22560 bayes= 10.2744 E= 3.3e+001 -9 -166 151 -285 110 80 -1140 -1140 27 34 -26 -53 68 -166 23 -27 174 -1140 -158 -1140 142 15 -1140 -1140 156 -1140 -26 -1140 68 51 -258 -53 127 -166 -1140 -5 -32 -34 42 14 -290 34 133 -127 -190 -1140 206 -1140 119 15 -158 -285 185 -1140 -1140 -1140 135 -1140 -99 -53 -90 115 42 -285 127 34 -258 -1140 110 34 -99 -1140 101 34 -99 -285 -9 -107 142 -285 -32 -7 -258 95 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 3.3e+001 0.259259 0.074074 0.629630 0.037037 0.592593 0.407407 0.000000 0.000000 0.333333 0.296296 0.185185 0.185185 0.444444 0.074074 0.259259 0.222222 0.925926 0.000000 0.074074 0.000000 0.740741 0.259259 0.000000 0.000000 0.814815 0.000000 0.185185 0.000000 0.444444 0.333333 0.037037 0.185185 0.666667 0.074074 0.000000 0.259259 0.222222 0.185185 0.296296 0.296296 0.037037 0.296296 0.555556 0.111111 0.074074 0.000000 0.925926 0.000000 0.629630 0.259259 0.074074 0.037037 1.000000 0.000000 0.000000 0.000000 0.703704 0.000000 0.111111 0.185185 0.148148 0.518519 0.296296 0.037037 0.666667 0.296296 0.037037 0.000000 0.592593 0.296296 0.111111 0.000000 0.555556 0.296296 0.111111 0.037037 0.259259 0.111111 0.592593 0.037037 0.222222 0.222222 0.037037 0.518519 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][AC][AC][AGT]A[AC]A[AC][AT][GTA][GC]G[AC]AA[CG][AC][AC][AC][GA][TAC] -------------------------------------------------------------------------------- Time 53.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9252 1.66e-02 137_[+3(4.34e-06)]_342 31529 2.52e-04 75_[+3(2.69e-06)]_217_\ [+1(8.85e-06)]_171 31684 7.34e-03 441_[+1(5.94e-06)]_43 6927 7.82e-03 72_[+3(1.31e-06)]_407 42799 2.82e-06 100_[+3(8.38e-07)]_286_\ [+1(8.94e-08)]_77 42972 2.76e-03 266_[+3(2.48e-07)]_213 46390 6.02e-04 132_[+1(2.39e-07)]_352 46648 5.42e-06 341_[+2(1.56e-08)]_120_\ [+1(1.25e-05)]_3 37254 1.22e-02 139_[+3(5.21e-06)]_340 38390 6.23e-07 440_[+1(7.01e-06)]_12_\ [+2(3.47e-09)]_12 48037 3.30e-01 500 43402 7.08e-01 500 43539 5.67e-01 500 41268 6.97e-03 14_[+3(4.34e-06)]_465 44363 2.84e-04 254_[+2(4.39e-05)]_91_\ [+1(1.20e-06)]_119 44501 5.77e-03 344_[+1(8.98e-07)]_140 10799 2.95e-06 55_[+2(1.35e-08)]_195_\ [+3(2.44e-05)]_209 11259 3.37e-02 115_[+3(1.33e-05)]_364 45111 2.38e-02 186_[+3(4.76e-06)]_293 45216 9.86e-03 168_[+3(1.99e-06)]_311 35054 1.11e-02 392_[+1(4.12e-06)]_92 35296 6.90e-02 296_[+3(1.55e-05)]_183 45698 1.09e-01 500 46135 1.63e-07 29_[+2(5.17e-05)]_136_\ [+2(1.89e-09)]_240_[+3(3.60e-06)]_34 46214 1.42e-04 278_[+1(4.03e-07)]_5_[+3(2.81e-05)]_\ 180 46264 6.89e-02 308_[+1(8.85e-06)]_176 42698 1.21e-01 500 31874 4.30e-01 500 31876 2.71e-02 198_[+3(5.70e-06)]_281 46895 2.10e-04 284_[+1(1.09e-05)]_104_\ [+3(1.05e-06)]_75 39506 1.00e-09 297_[+2(7.71e-13)]_92_\ [+3(2.81e-05)]_70 34899 1.95e-02 298_[+1(4.98e-06)]_186 36402 4.99e-04 59_[+1(1.42e-05)]_122_\ [+3(2.43e-06)]_282 44830 7.61e-05 97_[+3(2.44e-05)]_162_\ [+1(6.63e-07)]_204 36434 3.38e-03 385_[+3(4.12e-07)]_94 36514 1.41e-01 500 37648 1.40e-01 500 43894 1.43e-05 9_[+3(1.99e-06)]_163_[+3(4.24e-05)]_\ 3_[+1(7.59e-06)]_27_[+2(5.83e-05)]_220 33005 1.50e-03 378_[+3(8.38e-05)]_20_\ [+3(6.04e-08)]_60 45822 2.39e-07 356_[+1(1.02e-05)]_12_\ [+3(1.83e-09)]_95 34528 5.72e-03 148_[+1(5.44e-06)]_336 37029 8.03e-08 310_[+2(7.71e-13)]_170 47034 1.20e-09 91_[+3(2.27e-05)]_202_\ [+2(1.41e-08)]_82_[+1(8.94e-08)]_68 34230 4.89e-04 357_[+3(4.76e-06)]_101_\ [+1(7.01e-06)]_5 33881 4.88e-05 361_[+3(8.09e-06)]_57_\ [+1(2.46e-06)]_45 35182 1.73e-01 500 45981 7.48e-04 40_[+3(1.09e-07)]_439 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************