******************************************************************************** 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/184/184.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31997 1.0000 500 1690 1.0000 500 46979 1.0000 500 54901 1.0000 500 15060 1.0000 500 30139 1.0000 500 30140 1.0000 500 39880 1.0000 500 52607 1.0000 500 50189 1.0000 500 18622 1.0000 500 44312 1.0000 500 44949 1.0000 500 20120 1.0000 500 46053 1.0000 500 12674 1.0000 500 31429 1.0000 500 38802 1.0000 500 48837 1.0000 500 36733 1.0000 500 35959 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/184/184.seqs.fa -oc motifs/184 -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= 21 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= 10500 N= 21 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.248 C 0.261 G 0.253 T 0.238 Background letter frequencies (from dataset with add-one prior applied): A 0.248 C 0.261 G 0.253 T 0.238 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 12 llr = 130 E-value = 7.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1::2::5::::: pos.-specific C 2:93:64::282 probability G ::131::1::1: matrix T 8a:39419a818 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 TTCCTCATTTCT consensus G TC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46053 439 6.10e-07 CTGTTTGCGG TTCGTTCTTTCT GCTTTCCTAT 35959 30 9.60e-07 AACCAGTTGT TTCCTCATTTCC GTAAGTAAAA 31997 450 1.43e-06 TTCTCTCCCG CTCGTCATTTCT TTGGCGTCAT 44312 367 1.78e-06 ACACTCTTTC CTCTTCCTTTCT TGCAACAAAG 30139 411 1.78e-06 TTGGGTTTCG TTCGTCTTTTCT TTACACCAAC 1690 450 2.43e-06 TCCGGTGCCG TTCTTTATTTCC AAAATACAGA 52607 344 3.11e-06 GGGCGTCCCC TTCATCATTCCT TGGTGAGCCT 39880 385 3.95e-06 TCTTCAGATA TTCCTTATTTTT TTTGCTAGGA 50189 401 6.94e-06 TGTCGCACTT TTGTTTCTTTCT CGTAGCATTT 48837 181 7.74e-06 TCCTTTCCTA TTCATCCGTTCT ATAAATGTCT 20120 63 1.19e-05 CCACGCATCG ATCCTCATTCCT GAATACATAA 54901 298 3.46e-05 CAGGAGTTCC TTCCGTCTTTGT TGACGCACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46053 6.1e-07 438_[+1]_50 35959 9.6e-07 29_[+1]_459 31997 1.4e-06 449_[+1]_39 44312 1.8e-06 366_[+1]_122 30139 1.8e-06 410_[+1]_78 1690 2.4e-06 449_[+1]_39 52607 3.1e-06 343_[+1]_145 39880 3.9e-06 384_[+1]_104 50189 6.9e-06 400_[+1]_88 48837 7.7e-06 180_[+1]_308 20120 1.2e-05 62_[+1]_426 54901 3.5e-05 297_[+1]_191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=12 46053 ( 439) TTCGTTCTTTCT 1 35959 ( 30) TTCCTCATTTCC 1 31997 ( 450) CTCGTCATTTCT 1 44312 ( 367) CTCTTCCTTTCT 1 30139 ( 411) TTCGTCTTTTCT 1 1690 ( 450) TTCTTTATTTCC 1 52607 ( 344) TTCATCATTCCT 1 39880 ( 385) TTCCTTATTTTT 1 50189 ( 401) TTGTTTCTTTCT 1 48837 ( 181) TTCATCCGTTCT 1 20120 ( 63) ATCCTCATTCCT 1 54901 ( 298) TTCCGTCTTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 10269 bayes= 10.1873 E= 7.1e+000 -157 -65 -1023 165 -1023 -1023 -1023 207 -1023 181 -160 -1023 -57 35 -2 7 -1023 -1023 -160 194 -1023 116 -1023 80 101 68 -1023 -151 -1023 -1023 -160 194 -1023 -1023 -1023 207 -1023 -65 -1023 180 -1023 167 -160 -151 -1023 -65 -1023 180 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 7.1e+000 0.083333 0.166667 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.916667 0.083333 0.000000 0.166667 0.333333 0.250000 0.250000 0.000000 0.000000 0.083333 0.916667 0.000000 0.583333 0.000000 0.416667 0.500000 0.416667 0.000000 0.083333 0.000000 0.000000 0.083333 0.916667 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.833333 0.083333 0.083333 0.000000 0.166667 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTC[CGT]T[CT][AC]TTTCT -------------------------------------------------------------------------------- Time 3.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 18 sites = 9 llr = 129 E-value = 6.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2:::::1:26:11:::6: pos.-specific C :4912:1:2:8::::11: probability G 83:9::3944::23123: matrix T :21:8a411:297797:a bits 2.1 * * 1.9 * * 1.7 * * * * 1.4 ** * * * * * Relative 1.2 * **** * ** * * Entropy 1.0 * **** * *** ** * (20.6 bits) 0.8 * **** * ******* * 0.6 * **** * ********* 0.4 ****** * ********* 0.2 ****************** 0.0 ------------------ Multilevel GCCGTTTGGACTTTTTAT consensus AG C G AGT GG GG sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 35959 307 4.45e-11 CAAAACATCC GCCGTTGGGACTTTTTAT CACATAAGAC 46053 173 1.71e-08 TTGCATAGTT GGCGTTTGTACTTTTTCT CGGACTGACG 52607 199 3.68e-08 GACGTTCCCG GGCGTTTGGGCAGTTTAT GCGTATCACG 30140 169 6.04e-08 ATCGAAAACA GGCGCTCGCACTTTTTGT AGAGAAAGCG 15060 185 1.47e-07 TCCAATCAAT ACCGTTTGGACTGGTCAT GACGGCATTG 1690 172 3.40e-07 CGGCAATGAC GTCGCTAGGGTTTGTTGT GGTGTGGTGA 44949 177 5.12e-07 TGTCGTGTCC GCCGTTGGAGTTTGGGAT TCCGGTGCGC 36733 37 5.45e-07 GTCTACGTTG ACTCTTTGAACTTTTTGT TACAAAGACT 44312 273 7.01e-07 TCCCATTGCT GTCGTTGTCGCTATTGAT TCACACTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35959 4.4e-11 306_[+2]_176 46053 1.7e-08 172_[+2]_310 52607 3.7e-08 198_[+2]_284 30140 6e-08 168_[+2]_314 15060 1.5e-07 184_[+2]_298 1690 3.4e-07 171_[+2]_311 44949 5.1e-07 176_[+2]_306 36733 5.5e-07 36_[+2]_446 44312 7e-07 272_[+2]_210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=18 seqs=9 35959 ( 307) GCCGTTGGGACTTTTTAT 1 46053 ( 173) GGCGTTTGTACTTTTTCT 1 52607 ( 199) GGCGTTTGGGCAGTTTAT 1 30140 ( 169) GGCGCTCGCACTTTTTGT 1 15060 ( 185) ACCGTTTGGACTGGTCAT 1 1690 ( 172) GTCGCTAGGGTTTGTTGT 1 44949 ( 177) GCCGTTGGAGTTTGGGAT 1 36733 ( 37) ACTCTTTGAACTTTTTGT 1 44312 ( 273) GTCGTTGTCGCTATTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 10143 bayes= 10.2714 E= 6.9e+000 -16 -982 162 -982 -982 77 40 -10 -982 177 -982 -110 -982 -123 181 -982 -982 -23 -982 170 -982 -982 -982 207 -115 -123 40 90 -982 -982 181 -110 -16 -23 81 -110 117 -982 81 -982 -982 158 -982 -10 -115 -982 -982 190 -115 -982 -19 148 -982 -982 40 148 -982 -982 -119 190 -982 -123 -19 148 117 -123 40 -982 -982 -982 -982 207 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 6.9e+000 0.222222 0.000000 0.777778 0.000000 0.000000 0.444444 0.333333 0.222222 0.000000 0.888889 0.000000 0.111111 0.000000 0.111111 0.888889 0.000000 0.000000 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 1.000000 0.111111 0.111111 0.333333 0.444444 0.000000 0.000000 0.888889 0.111111 0.222222 0.222222 0.444444 0.111111 0.555556 0.000000 0.444444 0.000000 0.000000 0.777778 0.000000 0.222222 0.111111 0.000000 0.000000 0.888889 0.111111 0.000000 0.222222 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.111111 0.888889 0.000000 0.111111 0.222222 0.666667 0.555556 0.111111 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][CGT]CG[TC]T[TG]G[GAC][AG][CT]T[TG][TG]T[TG][AG]T -------------------------------------------------------------------------------- Time 8.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 6 llr = 87 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::77:2:::2::::2 pos.-specific C ::::a::::3a33:: probability G 5:23:7::22:7::: matrix T 5a2::2aa83::7a8 bits 2.1 * ** * 1.9 * * ** * * 1.7 * * ** * * 1.4 * * *** * ** Relative 1.2 * * *** * ** Entropy 1.0 ** ** *** ***** (20.8 bits) 0.8 ********* ***** 0.6 ********* ***** 0.4 ********* ***** 0.2 ********* ***** 0.0 --------------- Multilevel GTAACGTTTCCGTTT consensus T G T CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 30139 379 9.93e-09 CGACTGTTTT GTAACGTTTTCCTTT TCTCGTGTTG 38802 473 4.93e-08 TGAATCTTCG GTAACGTTGTCGTTT GGTGCCGACC 46979 200 1.11e-07 ACTGTGACGG TTAACGTTTACGTTA TGTATGCACA 1690 291 2.00e-07 GTTGGCAACC TTGGCGTTTCCCTTT CTGGTACACT 31997 471 3.32e-07 TTTGGCGTCA TTTACTTTTCCGCTT CGCCTACTAT 50189 414 3.83e-07 TTTCTTTCTC GTAGCATTTGCGCTT GAATTGTAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 30139 9.9e-09 378_[+3]_107 38802 4.9e-08 472_[+3]_13 46979 1.1e-07 199_[+3]_286 1690 2e-07 290_[+3]_195 31997 3.3e-07 470_[+3]_15 50189 3.8e-07 413_[+3]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=6 30139 ( 379) GTAACGTTTTCCTTT 1 38802 ( 473) GTAACGTTGTCGTTT 1 46979 ( 200) TTAACGTTTACGTTA 1 1690 ( 291) TTGGCGTTTCCCTTT 1 31997 ( 471) TTTACTTTTCCGCTT 1 50189 ( 414) GTAGCATTTGCGCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 10206 bayes= 11.179 E= 1.7e+003 -923 -923 98 107 -923 -923 -923 207 143 -923 -60 -52 143 -923 40 -923 -923 194 -923 -923 -57 -923 140 -52 -923 -923 -923 207 -923 -923 -923 207 -923 -923 -60 180 -57 35 -60 48 -923 194 -923 -923 -923 35 140 -923 -923 35 -923 148 -923 -923 -923 207 -57 -923 -923 180 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6 E= 1.7e+003 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.666667 0.000000 0.166667 0.166667 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.166667 0.333333 0.166667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT]TA[AG]CGTTT[CT]C[GC][TC]TT -------------------------------------------------------------------------------- Time 11.92 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31997 1.43e-05 449_[+1(1.43e-06)]_9_[+3(3.32e-07)]_\ 15 1690 6.26e-09 171_[+2(3.40e-07)]_101_\ [+3(2.00e-07)]_144_[+1(2.43e-06)]_39 46979 6.33e-05 199_[+3(1.11e-07)]_286 54901 6.47e-02 297_[+1(3.46e-05)]_191 15060 1.90e-03 184_[+2(1.47e-07)]_298 30139 6.03e-07 378_[+3(9.93e-09)]_17_\ [+1(1.78e-06)]_78 30140 2.89e-04 168_[+2(6.04e-08)]_314 39880 9.66e-03 384_[+1(3.95e-06)]_104 52607 4.32e-06 198_[+2(3.68e-08)]_105_\ [+1(2.16e-05)]_10_[+1(3.11e-06)]_145 50189 1.53e-05 400_[+1(6.94e-06)]_1_[+3(3.83e-07)]_\ 72 18622 3.04e-01 500 44312 5.13e-06 272_[+2(7.01e-07)]_76_\ [+1(1.78e-06)]_122 44949 4.12e-03 176_[+2(5.12e-07)]_306 20120 1.12e-01 62_[+1(1.19e-05)]_426 46053 5.14e-08 172_[+2(1.71e-08)]_228_\ [+2(8.05e-05)]_2_[+1(6.10e-07)]_50 12674 9.99e-01 500 31429 7.73e-01 500 38802 3.01e-04 310_[+3(6.61e-06)]_147_\ [+3(4.93e-08)]_13 48837 1.22e-02 180_[+1(7.74e-06)]_308 36733 1.38e-03 36_[+2(5.45e-07)]_446 35959 1.27e-09 29_[+1(9.60e-07)]_265_\ [+2(4.45e-11)]_176 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************