******************************************************************************** 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/179/179.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21829 1.0000 500 47934 1.0000 500 14857 1.0000 500 43565 1.0000 500 15977 1.0000 500 40199 1.0000 500 49556 1.0000 500 49644 1.0000 500 10830 1.0000 500 45846 1.0000 500 36103 1.0000 500 44429 1.0000 500 44924 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/179/179.seqs.fa -oc motifs/179 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.232 G 0.241 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.232 G 0.241 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 18 sites = 7 llr = 109 E-value = 1.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7::1:::::::1:::::: pos.-specific C 3:94::a616:313:::1 probability G ::::31:::::343:4:: matrix T :a1479:494a344a6a9 bits 2.1 * 1.9 * * * * * 1.7 * * * * * 1.5 ** * * * * Relative 1.3 ** ** * * * ** Entropy 1.1 *** ******* **** (22.4 bits) 0.8 *** ******* **** 0.6 *********** * **** 0.4 *********** ****** 0.2 *********** ****** 0.0 ------------------ Multilevel ATCCTTCCTCTCGTTTTT consensus C TG T T GTC G sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 45846 311 1.48e-09 TTATCTATCG ATCCTTCCTTTCGTTGTT GCATATTATC 49644 50 2.52e-09 CTTCGCCGTC ATCCTTCTTCTTGCTTTT AGGAGGCATT 21829 416 3.15e-09 CACTGAGAAT ATCCTTCCTTTTTGTTTT GTGGGTCCTC 14857 23 6.93e-08 CACTGAGAGT ATCTTTCCTCTGCGTTTC GTGTGTCCTG 36103 375 1.35e-07 ACCCTTGAAA ATCTGGCTTCTATTTTTT CATTTGCGCC 40199 325 1.69e-07 AAACGGTATA CTTTTTCTTTTGTCTGTT TGAAACGGAA 10830 158 2.28e-07 CAGCGAGGAT CTCAGTCCCCTCGTTGTT GCGGATGGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45846 1.5e-09 310_[+1]_172 49644 2.5e-09 49_[+1]_433 21829 3.2e-09 415_[+1]_67 14857 6.9e-08 22_[+1]_460 36103 1.4e-07 374_[+1]_108 40199 1.7e-07 324_[+1]_158 10830 2.3e-07 157_[+1]_325 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=18 seqs=7 45846 ( 311) ATCCTTCCTTTCGTTGTT 1 49644 ( 50) ATCCTTCTTCTTGCTTTT 1 21829 ( 416) ATCCTTCCTTTTTGTTTT 1 14857 ( 23) ATCTTTCCTCTGCGTTTC 1 36103 ( 375) ATCTGGCTTCTATTTTTT 1 40199 ( 325) CTTTTTCTTTTGTCTGTT 1 10830 ( 158) CTCAGTCCCCTCGTTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 6279 bayes= 9.65105 E= 1.9e+001 142 30 -945 -945 -945 -945 -945 194 -945 189 -945 -87 -90 89 -945 71 -945 -945 24 145 -945 -945 -75 171 -945 211 -945 -945 -945 130 -945 71 -945 -70 -945 171 -945 130 -945 71 -945 -945 -945 194 -90 30 24 13 -945 -70 83 71 -945 30 24 71 -945 -945 -945 194 -945 -945 83 113 -945 -945 -945 194 -945 -70 -945 171 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 7 E= 1.9e+001 0.714286 0.285714 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.142857 0.142857 0.428571 0.000000 0.428571 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.000000 0.428571 0.000000 0.142857 0.000000 0.857143 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.000000 1.000000 0.142857 0.285714 0.285714 0.285714 0.000000 0.142857 0.428571 0.428571 0.000000 0.285714 0.285714 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC]TC[CT][TG]TC[CT]T[CT]T[CGT][GT][TCG]T[TG]TT -------------------------------------------------------------------------------- Time 1.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 118 E-value = 6.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :76:7::a::436:1:6:93: pos.-specific C 33:a3:6:11:7:9:1:3::: probability G 7:1::33:4:6:11:9:6:6: matrix T ::3::71:49::3:9:4111a bits 2.1 * 1.9 * * * 1.7 * * * 1.5 * * * * * Relative 1.3 * * * * * *** * * Entropy 1.1 ** *** * *** *** * * (24.3 bits) 0.8 ** *** * *** **** * * 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAACATCAGTGCACTGAGAGT consensus CCT CGG T AAT TC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 14857 2 5.44e-12 A GAACATGATTGCACTGAGAGT ATCTTTCCTC 21829 395 3.84e-11 AATACTTGTA GAACATGATTGCACTGAGAAT ATCCTTCCTT 49644 413 1.62e-09 TCAGACTCTC GCACATTAGTACACTGTCAGT ATCCCGAAAC 10830 386 5.15e-09 TTATGAAGGA CAACCTCACTGATCTGAGAGT CATGCCTTGT 40199 46 7.62e-08 CTTCTTCCGT CAGCAGCAGTACTCTGTTTGT TCTTTGATCT 44429 82 9.86e-08 CGATTTTAAG GATCCGCATTGCGGTGTCATT TACTCACTCG 15977 9 1.74e-07 CCATGCAG GCTCATCAGCAAACACAGAAT GCTTCGAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14857 5.4e-12 1_[+2]_478 21829 3.8e-11 394_[+2]_85 49644 1.6e-09 412_[+2]_67 10830 5.1e-09 385_[+2]_94 40199 7.6e-08 45_[+2]_434 44429 9.9e-08 81_[+2]_398 15977 1.7e-07 8_[+2]_471 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 14857 ( 2) GAACATGATTGCACTGAGAGT 1 21829 ( 395) GAACATGATTGCACTGAGAAT 1 49644 ( 413) GCACATTAGTACACTGTCAGT 1 10830 ( 386) CAACCTCACTGATCTGAGAGT 1 40199 ( 46) CAGCAGCAGTACTCTGTTTGT 1 44429 ( 82) GATCCGCATTGCGGTGTCATT 1 15977 ( 9) GCTCATCAGCAAACACAGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 10.4046 E= 6.2e+001 -945 30 157 -945 142 30 -945 -945 110 -945 -75 13 -945 211 -945 -945 142 30 -945 -945 -945 -945 24 145 -945 130 24 -87 191 -945 -945 -945 -945 -70 83 71 -945 -70 -945 171 69 -945 124 -945 10 162 -945 -945 110 -945 -75 13 -945 189 -75 -945 -90 -945 -945 171 -945 -70 183 -945 110 -945 -945 71 -945 30 124 -87 169 -945 -945 -87 10 -945 124 -87 -945 -945 -945 194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 6.2e+001 0.000000 0.285714 0.714286 0.000000 0.714286 0.285714 0.000000 0.000000 0.571429 0.000000 0.142857 0.285714 0.000000 1.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.571429 0.285714 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.428571 0.428571 0.000000 0.142857 0.000000 0.857143 0.428571 0.000000 0.571429 0.000000 0.285714 0.714286 0.000000 0.000000 0.571429 0.000000 0.142857 0.285714 0.000000 0.857143 0.142857 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.142857 0.857143 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 0.285714 0.571429 0.142857 0.857143 0.000000 0.000000 0.142857 0.285714 0.000000 0.571429 0.142857 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][AC][AT]C[AC][TG][CG]A[GT]T[GA][CA][AT]CTG[AT][GC]A[GA]T -------------------------------------------------------------------------------- Time 2.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 14 sites = 4 llr = 67 E-value = 7.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::::::3::: pos.-specific C ::a:3::a3a:5:: probability G :a:a3:::::8::a matrix T a:::5aa:8::5a: bits 2.1 *** * * * 1.9 **** *** * ** 1.7 **** *** * ** 1.5 **** *** * ** Relative 1.3 **** ****** ** Entropy 1.1 **** ********* (24.1 bits) 0.8 **** ********* 0.6 **** ********* 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel TGCGTTTCTCGCTG consensus C C AT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 14857 59 3.09e-09 TGTGGGCCTA TGCGTTTCTCGCTG TACAGCGGCC 43565 92 1.85e-08 CGGTCGTTCC TGCGGTTCTCGTTG ACGTTGGTCG 21829 461 2.77e-08 CATCGGCCTT TGCGTTTCTCACTG TACAGCGGCC 44429 172 4.83e-08 AATTGCTACA TGCGCTTCCCGTTG GACGGTATCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14857 3.1e-09 58_[+3]_428 43565 1.8e-08 91_[+3]_395 21829 2.8e-08 460_[+3]_26 44429 4.8e-08 171_[+3]_315 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=4 14857 ( 59) TGCGTTTCTCGCTG 1 43565 ( 92) TGCGGTTCTCGTTG 1 21829 ( 461) TGCGTTTCTCACTG 1 44429 ( 172) TGCGCTTCCCGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 6331 bayes= 10.6273 E= 7.7e+001 -865 -865 -865 193 -865 -865 205 -865 -865 211 -865 -865 -865 -865 205 -865 -865 11 5 93 -865 -865 -865 193 -865 -865 -865 193 -865 211 -865 -865 -865 11 -865 152 -865 211 -865 -865 -9 -865 163 -865 -865 111 -865 93 -865 -865 -865 193 -865 -865 205 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 4 E= 7.7e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TGCG[TCG]TTC[TC]C[GA][CT]TG -------------------------------------------------------------------------------- Time 4.29 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21829 3.57e-16 394_[+2(3.84e-11)]_[+1(3.15e-09)]_\ 27_[+3(2.77e-08)]_26 47934 7.69e-01 500 14857 1.30e-16 1_[+2(5.44e-12)]_[+1(6.93e-08)]_18_\ [+3(3.09e-09)]_428 43565 2.31e-04 91_[+3(1.85e-08)]_395 15977 3.61e-03 8_[+2(1.74e-07)]_471 40199 5.09e-07 45_[+2(7.62e-08)]_258_\ [+1(1.69e-07)]_158 49556 6.02e-01 500 49644 2.99e-10 49_[+1(2.52e-09)]_345_\ [+2(1.62e-09)]_67 10830 4.61e-08 157_[+1(2.28e-07)]_210_\ [+2(5.15e-09)]_94 45846 3.53e-05 310_[+1(1.48e-09)]_172 36103 6.04e-04 374_[+1(1.35e-07)]_108 44429 4.43e-08 81_[+2(9.86e-08)]_69_[+3(4.83e-08)]_\ 63_[+2(4.23e-06)]_231 44924 7.16e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************