******************************************************************************** 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/160/160.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 5588 1.0000 500 7957 1.0000 500 45934 1.0000 500 36776 1.0000 500 38403 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/160/160.seqs.fa -oc motifs/160 -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= 5 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= 2500 N= 5 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.254 C 0.252 G 0.230 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.254 C 0.252 G 0.230 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 5 llr = 90 E-value = 1.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::2::::::8:::::8:24: pos.-specific C 888:2:62a:2:446:2a24a probability G :::::442:a:4:2:a::::: matrix T 222886:6:::6644:::62: bits 2.1 * * 1.9 ** * * * 1.7 ** * * * 1.5 ** * * * Relative 1.3 ***** *** *** * Entropy 1.1 ******* ***** **** * (26.1 bits) 0.8 ******* ***** **** * 0.6 ************* ***** * 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCCTTTCTCGATTCCGACTAC consensus TTTACGGC CGCTT C AC sequence G G CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38403 177 6.33e-13 GATGATCCCC CCCTTTCTCGATTCCGACTCC GGGACGATGC 7957 393 2.50e-09 AGAGCGCGCC CCCTTTCTCGAGCTTGCCAAC GAGGAAGCGA 45934 396 6.47e-09 CAACAACAAC CCCACGGGCGATCCCGACTCC CAGGACAGCC 5588 223 7.42e-09 GGACAATGCT CTCTTGCCCGAGTTTGACCAC TTGTATCTCG 36776 241 1.87e-08 TTTAATGTGG TCTTTTGTCGCTTGCGACTTC AACTTTGTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38403 6.3e-13 176_[+1]_303 7957 2.5e-09 392_[+1]_87 45934 6.5e-09 395_[+1]_84 5588 7.4e-09 222_[+1]_257 36776 1.9e-08 240_[+1]_239 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=5 38403 ( 177) CCCTTTCTCGATTCCGACTCC 1 7957 ( 393) CCCTTTCTCGAGCTTGCCAAC 1 45934 ( 396) CCCACGGGCGATCCCGACTCC 1 5588 ( 223) CTCTTGCCCGAGTTTGACCAC 1 36776 ( 241) TCTTTTGTCGCTTGCGACTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2400 bayes= 8.90388 E= 1.2e+002 -897 166 -897 -40 -897 166 -897 -40 -897 166 -897 -40 -34 -897 -897 160 -897 -33 -897 160 -897 -897 80 118 -897 125 80 -897 -897 -33 -20 118 -897 199 -897 -897 -897 -897 212 -897 165 -33 -897 -897 -897 -897 80 118 -897 67 -897 118 -897 67 -20 60 -897 125 -897 60 -897 -897 212 -897 165 -33 -897 -897 -897 199 -897 -897 -34 -33 -897 118 65 67 -897 -40 -897 199 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.2e+002 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.400000 0.600000 0.000000 0.600000 0.400000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.400000 0.000000 0.600000 0.000000 0.400000 0.200000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.600000 0.400000 0.400000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CT][CT][TA][TC][TG][CG][TCG]CG[AC][TG][TC][CTG][CT]G[AC]C[TAC][ACT]C -------------------------------------------------------------------------------- Time 0.28 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 84 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a::4:44:242a:44:684:a pos.-specific C :4:24::::2::222:224:: probability G :6a226:8828:6:4a2:2a: matrix T :::24:62:2::24::::::: bits 2.1 * * * 1.9 * * * * ** 1.7 * * * * ** 1.5 * * * * ** Relative 1.3 * * ** ** * * ** Entropy 1.1 *** **** ** * * ** (24.2 bits) 0.8 *** **** ** * * ** 0.6 *** **** *** *** ** 0.4 *** ***** *********** 0.2 *** ***** *********** 0.0 --------------------- Multilevel AGGACGTGGAGAGAAGAAAGA consensus C CTAATACA CTG CCC sequence GG G TCC G G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38403 463 5.94e-10 GTCCGAATAG AGGGTGAGGAGAGAAGGAAGA ATTGCTTCTT 45934 197 1.43e-09 GATCACGACG ACGACGTGGAAAGCGGAACGA ACGCGCACAC 36776 83 2.11e-09 GCGGTTGACA AGGATATTGCGAGAAGAACGA TGACAGTGGT 5588 17 4.61e-08 ACTTGGAATG ACGCCGTGGGGATTCGCAGGA TCGTAGACGA 7957 101 1.15e-07 ATCTTTCAAC AGGTGAAGATGACTGGACAGA AGAAGATATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38403 5.9e-10 462_[+2]_17 45934 1.4e-09 196_[+2]_283 36776 2.1e-09 82_[+2]_397 5588 4.6e-08 16_[+2]_463 7957 1.1e-07 100_[+2]_379 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 38403 ( 463) AGGGTGAGGAGAGAAGGAAGA 1 45934 ( 197) ACGACGTGGAAAGCGGAACGA 1 36776 ( 83) AGGATATTGCGAGAAGAACGA 1 5588 ( 17) ACGCCGTGGGGATTCGCAGGA 1 7957 ( 101) AGGTGAAGATGACTGGACAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2400 bayes= 8.90388 E= 1.8e+002 197 -897 -897 -897 -897 67 138 -897 -897 -897 212 -897 65 -33 -20 -40 -897 67 -20 60 65 -897 138 -897 65 -897 -897 118 -897 -897 180 -40 -34 -897 180 -897 65 -33 -20 -40 -34 -897 180 -897 197 -897 -897 -897 -897 -33 138 -40 65 -33 -897 60 65 -33 80 -897 -897 -897 212 -897 124 -33 -20 -897 165 -33 -897 -897 65 67 -20 -897 -897 -897 212 -897 197 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.8e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.400000 0.200000 0.400000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.800000 0.200000 0.200000 0.000000 0.800000 0.000000 0.400000 0.200000 0.200000 0.200000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.200000 0.400000 0.200000 0.000000 0.400000 0.400000 0.200000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GC]G[ACGT][CTG][GA][TA][GT][GA][ACGT][GA]A[GCT][ATC][AGC]G[ACG][AC][ACG]GA -------------------------------------------------------------------------------- Time 0.54 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 4 llr = 76 E-value = 2.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::83:33:::3::a:::3:a pos.-specific C 8::8::53a::5::a3:::: probability G 3a::a::5:5::a::3a38: matrix T ::3::833:585:::5:53: bits 2.1 * * * * 1.9 * * * *** * * 1.7 * * * *** * * 1.5 * * * *** * * Relative 1.3 ** ** * *** * ** Entropy 1.1 ****** *** *** * ** (27.4 bits) 0.8 ****** ******* * ** 0.6 ****** ******** * ** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CGACGTCGCGTCGACTGTGA consensus G TA AAC TAT C AT sequence TT G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 36776 393 3.05e-12 CCAATTCGAT CGACGTCGCTTTGACTGTGA AAAAGGAAGA 38403 199 1.15e-09 TCCGACTCCG GGACGATGCTTTGACTGTGA ATGGTGTTCC 45934 292 4.15e-09 ACAGACGCTA CGACGTCCCGACGACGGATA CGGGACATTG 7957 162 7.03e-09 GGAAAAACTG CGTAGTATCGTCGACCGGGA TGGATCCTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36776 3.1e-12 392_[+3]_88 38403 1.2e-09 198_[+3]_282 45934 4.2e-09 291_[+3]_189 7957 7e-09 161_[+3]_319 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=4 36776 ( 393) CGACGTCGCTTTGACTGTGA 1 38403 ( 199) GGACGATGCTTTGACTGTGA 1 45934 ( 292) CGACGTCCCGACGACGGATA 1 7957 ( 162) CGTAGTATCGTCGACCGGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2405 bayes= 9.96735 E= 2.2e+002 -865 157 12 -865 -865 -865 212 -865 156 -865 -865 -8 -2 157 -865 -865 -865 -865 212 -865 -2 -865 -865 150 -2 99 -865 -8 -865 -1 112 -8 -865 199 -865 -865 -865 -865 112 92 -2 -865 -865 150 -865 99 -865 92 -865 -865 212 -865 197 -865 -865 -865 -865 199 -865 -865 -865 -1 12 92 -865 -865 212 -865 -2 -865 12 92 -865 -865 171 -8 197 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 2.2e+002 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.250000 0.000000 0.250000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.250000 0.000000 0.000000 0.750000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.000000 0.750000 0.250000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG]G[AT][CA]G[TA][CAT][GCT]C[GT][TA][CT]GAC[TCG]G[TAG][GT]A -------------------------------------------------------------------------------- Time 0.77 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5588 4.07e-09 16_[+2(4.61e-08)]_185_\ [+1(7.42e-09)]_257 7957 1.53e-13 100_[+2(1.15e-07)]_40_\ [+3(7.03e-09)]_211_[+1(2.50e-09)]_87 45934 3.59e-15 196_[+2(1.43e-09)]_74_\ [+3(4.15e-09)]_84_[+1(6.47e-09)]_84 36776 1.46e-17 82_[+2(2.11e-09)]_137_\ [+1(1.87e-08)]_131_[+3(3.05e-12)]_88 38403 6.60e-20 176_[+1(6.33e-13)]_1_[+3(1.15e-09)]_\ 244_[+2(5.94e-10)]_17 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************