******************************************************************************** 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/464/464.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46935 1.0000 500 49800 1.0000 500 40381 1.0000 500 44711 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/464/464.seqs.fa -oc motifs/464 -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= 4 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= 2000 N= 4 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.245 C 0.221 G 0.246 T 0.287 Background letter frequencies (from dataset with add-one prior applied): A 0.246 C 0.221 G 0.247 T 0.287 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 4 llr = 49 E-value = 9.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::::3:::: pos.-specific C ::33a5a8a::8 probability G 3::5:3:::::3 matrix T 8a83:3:::aa: bits 2.2 * * * 2.0 * * * 1.7 * * * *** 1.5 * * * *** Relative 1.3 * * ****** Entropy 1.1 *** * ****** (17.8 bits) 0.9 *** * ****** 0.7 *** * ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTGCCCCCTTC consensus G CC G A G sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 40381 486 2.77e-07 AACACCGCCG TTCGCCCCCTTC GAA 49800 369 1.36e-06 CGTGAGCAAA GTTGCTCCCTTC AGCCAACGAG 46935 405 1.74e-06 GCTGGAGCTC TTTTCCCACTTC TGGTTGGTAA 44711 87 2.58e-06 TGGGGCTAAT TTTCCGCCCTTG GAAAGGCTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40381 2.8e-07 485_[+1]_3 49800 1.4e-06 368_[+1]_120 46935 1.7e-06 404_[+1]_84 44711 2.6e-06 86_[+1]_402 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=4 40381 ( 486) TTCGCCCCCTTC 1 49800 ( 369) GTTGCTCCCTTC 1 46935 ( 405) TTTTCCCACTTC 1 44711 ( 87) TTTCCGCCCTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1956 bayes= 8.93074 E= 9.2e+002 -865 -865 2 138 -865 -865 -865 180 -865 18 -865 138 -865 18 102 -20 -865 217 -865 -865 -865 118 2 -20 -865 217 -865 -865 3 176 -865 -865 -865 217 -865 -865 -865 -865 -865 180 -865 -865 -865 180 -865 176 2 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 4 E= 9.2e+002 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG]T[TC][GCT]C[CGT]C[CA]CTT[CG] -------------------------------------------------------------------------------- Time 0.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 4 llr = 50 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::33:3:3 pos.-specific C :::3:a:8:::8 probability G :aa:::5::88: matrix T a::8a:3:a:3: bits 2.2 * 2.0 ** * 1.7 *** ** * 1.5 *** ** * Relative 1.3 *** ** *** * Entropy 1.1 ****** ***** (18.2 bits) 0.9 ****** ***** 0.7 ****** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TGGTTCGCTGGC consensus C AA ATA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 49800 176 2.64e-07 AGTGTACGTG TGGCTCGCTGGC AAAAGATAGA 46935 61 1.10e-06 ATTCTCCAGC TGGTTCACTGTC GATAGCATGC 44711 34 1.38e-06 CTGGGCTGAT TGGTTCTCTGGA CCGGGATTTT 40381 90 1.69e-06 ACTATGTCAA TGGTTCGATAGC CAGTACATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49800 2.6e-07 175_[+2]_313 46935 1.1e-06 60_[+2]_428 44711 1.4e-06 33_[+2]_455 40381 1.7e-06 89_[+2]_399 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=4 49800 ( 176) TGGCTCGCTGGC 1 46935 ( 61) TGGTTCACTGTC 1 44711 ( 34) TGGTTCTCTGGA 1 40381 ( 90) TGGTTCGATAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1956 bayes= 8.93074 E= 1.6e+003 -865 -865 -865 180 -865 -865 202 -865 -865 -865 202 -865 -865 18 -865 138 -865 -865 -865 180 -865 217 -865 -865 3 -865 102 -20 3 176 -865 -865 -865 -865 -865 180 3 -865 160 -865 -865 -865 160 -20 3 176 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 4 E= 1.6e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.750000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TGG[TC]TC[GAT][CA]T[GA][GT][CA] -------------------------------------------------------------------------------- Time 0.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 4 llr = 60 E-value = 2.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::3::::::::388:: pos.-specific C :88:a83:8:3::3:: probability G :::8::5::a83::5a matrix T a3:3:33a3::53:5: bits 2.2 * 2.0 * * * 1.7 * * * * * 1.5 * * * * * Relative 1.3 *** ** **** * * Entropy 1.1 ****** **** ** * (21.6 bits) 0.9 ****** **** **** 0.7 ****** **** **** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TCCGCCGTCGGTAAGG consensus TAT TC T CATCT sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 40381 325 1.34e-09 TCTCCACATT TCCGCCGTCGGGAATG ATCAGAGTGC 44711 306 2.69e-08 GGGCTATTTT TCCGCCCTTGGAAAGG CTGTTTGAGA 46935 304 2.75e-07 GGTGCGTGTG TCATCCGTCGCTACTG TCCTTTGTCA 49800 235 3.23e-07 CGAAAGTTTC TTCGCTTTCGGTTAGG GCTTTGGACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40381 1.3e-09 324_[+3]_160 44711 2.7e-08 305_[+3]_179 46935 2.8e-07 303_[+3]_181 49800 3.2e-07 234_[+3]_250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=4 40381 ( 325) TCCGCCGTCGGGAATG 1 44711 ( 306) TCCGCCCTTGGAAAGG 1 46935 ( 304) TCATCCGTCGCTACTG 1 49800 ( 235) TTCGCTTTCGGTTAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1940 bayes= 8.91886 E= 2.3e+003 -865 -865 -865 180 -865 176 -865 -20 3 176 -865 -865 -865 -865 160 -20 -865 217 -865 -865 -865 176 -865 -20 -865 18 102 -20 -865 -865 -865 180 -865 176 -865 -20 -865 -865 202 -865 -865 18 160 -865 3 -865 2 80 161 -865 -865 -20 161 18 -865 -865 -865 -865 102 80 -865 -865 202 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 2.3e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.500000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.250000 0.500000 0.750000 0.000000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CT][CA][GT]C[CT][GCT]T[CT]G[GC][TAG][AT][AC][GT]G -------------------------------------------------------------------------------- Time 0.46 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46935 1.83e-08 60_[+2(1.10e-06)]_231_\ [+3(2.75e-07)]_85_[+1(1.74e-06)]_84 49800 4.57e-09 175_[+2(2.64e-07)]_47_\ [+3(3.23e-07)]_118_[+1(1.36e-06)]_120 40381 3.54e-11 89_[+2(1.69e-06)]_223_\ [+3(1.34e-09)]_145_[+1(2.77e-07)]_3 44711 3.83e-09 33_[+2(1.38e-06)]_43_[+3(2.69e-08)]_\ 146_[+2(3.98e-05)]_43_[+3(2.69e-08)]_179 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************