******************************************************************************** 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/128/128.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 39046 1.0000 500 49041 1.0000 500 41386 1.0000 500 49321 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/128/128.seqs.fa -oc motifs/128 -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 0.269 C 0.225 G 0.221 T 0.286 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.225 G 0.221 T 0.286 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 4 llr = 63 E-value = 1.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::::3::33:3:: pos.-specific C ::::8::383:::53: probability G a8:a::a33885838a matrix T :3a:3a:3:::33::: bits 2.2 * * * * 2.0 * * * * 1.7 * ** ** * 1.5 * ** ** * Relative 1.3 ******* *** * ** Entropy 1.1 ******* *** * ** (22.6 bits) 0.9 ******* *** * ** 0.7 ******* *** **** 0.4 ******* ******** 0.2 ******* ******** 0.0 ---------------- Multilevel GGTGCTGACGGGGCGG consensus T T CGCAATAC sequence G T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 49321 44 3.35e-09 AAAGGCATCG GGTGCTGACGGGTCGG AATCCGGGAA 49041 136 2.80e-08 CTTACTTTTA GTTGCTGGGGGGGGGG GGGGGGGAGA 39046 358 2.80e-08 TTTTCCTGAC GGTGCTGCCGGTGACG ACGGGAATCA 41386 61 1.80e-07 GCAACAAAAG GGTGTTGTCCAAGCGG ACACCAGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49321 3.3e-09 43_[+1]_441 49041 2.8e-08 135_[+1]_349 39046 2.8e-08 357_[+1]_127 41386 1.8e-07 60_[+1]_424 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=4 49321 ( 44) GGTGCTGACGGGTCGG 1 49041 ( 136) GTTGCTGGGGGGGGGG 1 39046 ( 358) GGTGCTGCCGGTGACG 1 41386 ( 61) GGTGTTGTCCAAGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1940 bayes= 9.65702 E= 1.3e+001 -865 -865 217 -865 -865 -865 176 -19 -865 -865 -865 180 -865 -865 217 -865 -865 174 -865 -19 -865 -865 -865 180 -865 -865 217 -865 -10 15 18 -19 -865 174 18 -865 -865 15 176 -865 -10 -865 176 -865 -10 -865 118 -19 -865 -865 176 -19 -10 115 18 -865 -865 15 176 -865 -865 -865 217 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 1.3e+001 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.250000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 0.750000 0.250000 0.250000 0.500000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[GT]TG[CT]TG[ACGT][CG][GC][GA][GAT][GT][CAG][GC]G -------------------------------------------------------------------------------- Time 0.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 4 llr = 63 E-value = 4.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3::83aa::::8::5: pos.-specific C ::8:3::a8a33:::a probability G 8:333:::::3:3:5: matrix T :a::3:::3:5:8a:: bits 2.2 * * * 2.0 *** * * 1.7 * *** * * * 1.5 * *** * * * Relative 1.3 *** ***** * * Entropy 1.1 **** ***** ***** (22.7 bits) 0.9 **** ***** ***** 0.7 **** ***** ***** 0.4 **** *********** 0.2 **** *********** 0.0 ---------------- Multilevel GTCAAAACCCTATTAC consensus A GGC T CCG G sequence G G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 41386 115 1.27e-08 GTACTTTGGG GTCAGAACTCTATTGC AACACGTTTG 49041 115 1.41e-08 ACGCTAGTTA GTCAAAACCCTCTTAC TTTTAGTTGC 39046 304 2.15e-08 GTCGTCGCGT GTCATAACCCCAGTGC TGGTCTCCTT 49321 194 1.86e-07 TGTAGGCAAC ATGGCAACCCGATTAC AGACTGAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41386 1.3e-08 114_[+2]_370 49041 1.4e-08 114_[+2]_370 39046 2.2e-08 303_[+2]_181 49321 1.9e-07 193_[+2]_291 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=4 41386 ( 115) GTCAGAACTCTATTGC 1 49041 ( 115) GTCAAAACCCTCTTAC 1 39046 ( 304) GTCATAACCCCAGTGC 1 49321 ( 194) ATGGCAACCCGATTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1940 bayes= 8.91886 E= 4.0e+002 -10 -865 176 -865 -865 -865 -865 180 -865 174 18 -865 148 -865 18 -865 -10 15 18 -19 189 -865 -865 -865 189 -865 -865 -865 -865 215 -865 -865 -865 174 -865 -19 -865 215 -865 -865 -865 15 18 80 148 15 -865 -865 -865 -865 18 139 -865 -865 -865 180 90 -865 118 -865 -865 215 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 4.0e+002 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.250000 0.250000 0.250000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]T[CG][AG][ACGT]AAC[CT]C[TCG][AC][TG]T[AG]C -------------------------------------------------------------------------------- Time 0.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 2 llr = 32 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::::a:::: pos.-specific C a::5:::::5:a probability G :aa:a:a:a5:: matrix T :::5:a::::a: bits 2.2 *** * * * * 2.0 *** * *** * 1.7 *** ***** ** 1.5 *** ***** ** Relative 1.3 *** ***** ** Entropy 1.1 ************ (22.9 bits) 0.9 ************ 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CGGCGTGAGCTC consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 39046 285 5.87e-08 GTCCGTTTCT CGGCGTGAGGTC GTCGCGTGTC 49321 81 1.33e-07 CGATTTTCTA CGGTGTGAGCTC CCGCTCGACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39046 5.9e-08 284_[+3]_204 49321 1.3e-07 80_[+3]_408 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=2 39046 ( 285) CGGCGTGAGGTC 1 49321 ( 81) CGGTGTGAGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1956 bayes= 9.93221 E= 1.4e+003 -765 215 -765 -765 -765 -765 217 -765 -765 -765 217 -765 -765 115 -765 80 -765 -765 217 -765 -765 -765 -765 180 -765 -765 217 -765 189 -765 -765 -765 -765 -765 217 -765 -765 115 117 -765 -765 -765 -765 180 -765 215 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 2 E= 1.4e+003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CGG[CT]GTGAG[CG]TC -------------------------------------------------------------------------------- Time 0.56 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39046 2.37e-12 284_[+3(5.87e-08)]_7_[+2(2.15e-08)]_\ 38_[+1(2.80e-08)]_127 49041 2.44e-08 114_[+2(1.41e-08)]_5_[+1(2.80e-08)]_\ 349 41386 4.05e-08 60_[+1(1.80e-07)]_38_[+2(1.27e-08)]_\ 370 49321 5.29e-12 43_[+1(3.35e-09)]_21_[+3(1.33e-07)]_\ 101_[+2(1.86e-07)]_291 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************