******************************************************************************** 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/379/379.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 6025 1.0000 500 47710 1.0000 500 49028 1.0000 500 49142 1.0000 500 49869 1.0000 500 43957 1.0000 500 37889 1.0000 500 38772 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/379/379.seqs.fa -oc motifs/379 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.241 C 0.244 G 0.235 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.241 C 0.245 G 0.235 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 6 llr = 105 E-value = 1.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::85a25378885:525:7:: pos.-specific C :3:::2::322:5:::::32: probability G 7725:527:::::a38:7::: matrix T 3::::23::::2::2:53:8a bits 2.1 * * 1.9 * * * 1.7 * * * 1.5 * * *** * * * Relative 1.3 ** * * *** * * ** Entropy 1.0 ***** ******* ****** (25.3 bits) 0.8 ***** ******* ****** 0.6 ***** *************** 0.4 ***** *************** 0.2 ********************* 0.0 --------------------- Multilevel GGAAAGAGAAAAAGAGAGATT consensus TC G TAC C G TTC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6025 453 5.25e-10 GGCTAAAAAG GGAAAGAAAAAACGTGATATT AATGCGTTGA 38772 317 6.68e-10 TCAATAACGT TGAAAGAACAAAAGAGTGCTT CGAGTCGAGA 43957 186 3.32e-09 GATGATTGGA GGGAAAGGAAAACGGGAGATT CTACGGGATC 49869 255 6.16e-09 TTCCGACGCG GGAGATAGAAAAAGGAAGACT ACCCCCCGAG 37889 97 1.42e-08 CTATATTCCC TCAGAGTGAACTCGAGTGATT ACCTTTTGTG 49028 376 2.36e-08 TCCTCGAAAA GCAGACTGCCAAAGAGTTCTT GAAGGTTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6025 5.3e-10 452_[+1]_27 38772 6.7e-10 316_[+1]_163 43957 3.3e-09 185_[+1]_294 49869 6.2e-09 254_[+1]_225 37889 1.4e-08 96_[+1]_383 49028 2.4e-08 375_[+1]_104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=6 6025 ( 453) GGAAAGAAAAAACGTGATATT 1 38772 ( 317) TGAAAGAACAAAAGAGTGCTT 1 43957 ( 186) GGGAAAGGAAAACGGGAGATT 1 49869 ( 255) GGAGATAGAAAAAGGAAGACT 1 37889 ( 97) TCAGAGTGAACTCGAGTGATT 1 49028 ( 376) GCAGACTGCCAAAGAGTTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 9.76773 E= 1.3e+001 -923 -923 150 26 -923 45 150 -923 179 -923 -50 -923 105 -923 109 -923 205 -923 -923 -923 -53 -55 109 -74 105 -923 -50 26 47 -923 150 -923 146 45 -923 -923 179 -55 -923 -923 179 -55 -923 -923 179 -923 -923 -74 105 103 -923 -923 -923 -923 209 -923 105 -923 50 -74 -53 -923 182 -923 105 -923 -923 84 -923 -923 150 26 146 45 -923 -923 -923 -55 -923 158 -923 -923 -923 184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.3e+001 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.666667 0.000000 0.833333 0.000000 0.166667 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.500000 0.166667 0.500000 0.000000 0.166667 0.333333 0.333333 0.000000 0.666667 0.000000 0.666667 0.333333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.333333 0.166667 0.166667 0.000000 0.833333 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.666667 0.333333 0.666667 0.333333 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][GC]A[AG]AG[AT][GA][AC]AAA[AC]G[AG]G[AT][GT][AC]TT -------------------------------------------------------------------------------- Time 0.62 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 5 llr = 85 E-value = 3.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :264:2::4:224:2:a26: pos.-specific C ::26:6::2:::22:2:4:: probability G 282::2:a:a4828:8:44: matrix T 8:::a:a:4:4:2:8::::a bits 2.1 * * * 1.9 * ** * * * 1.7 * ** * * * 1.5 * * ** * * * * Relative 1.3 ** * ** * * **** * Entropy 1.0 ** ** ** * * **** ** (24.6 bits) 0.8 ** ** ** * * **** ** 0.6 ******** * * ******* 0.4 ************ ******* 0.2 ************ ******* 0.0 -------------------- Multilevel TGACTCTGAGGGAGTGACAT consensus GACA A T TACCAC GG sequence G G C A G A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 47710 3 1.77e-11 TG TGACTCTGTGGGAGTGAGGT TCGCAGTCGA 6025 90 6.39e-10 GACCTTTGAG TGGCTCTGAGTGTGTGAGAT GTCAGGTCGT 49142 185 2.81e-08 TCGATGTGCA TGCATCTGTGAGCGAGAAAT CTTCCATTCA 37889 9 3.01e-08 CTCGCAAT TGACTGTGAGTAGCTGACGT CAATATGGTC 38772 59 6.50e-08 ATATTGCTAT GAAATATGCGGGAGTCACAT ACAGTTTTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47710 1.8e-11 2_[+2]_478 6025 6.4e-10 89_[+2]_391 49142 2.8e-08 184_[+2]_296 37889 3e-08 8_[+2]_472 38772 6.5e-08 58_[+2]_422 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=5 47710 ( 3) TGACTCTGTGGGAGTGAGGT 1 6025 ( 90) TGGCTCTGAGTGTGTGAGAT 1 49142 ( 185) TGCATCTGTGAGCGAGAAAT 1 37889 ( 9) TGACTGTGAGTAGCTGACGT 1 38772 ( 59) GAAATATGCGGGAGTCACAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 3848 bayes= 10.5304 E= 3.8e+002 -897 -897 -23 152 -27 -897 176 -897 131 -29 -23 -897 73 129 -897 -897 -897 -897 -897 184 -27 129 -23 -897 -897 -897 -897 184 -897 -897 209 -897 73 -29 -897 52 -897 -897 209 -897 -27 -897 76 52 -27 -897 176 -897 73 -29 -23 -48 -897 -29 176 -897 -27 -897 -897 152 -897 -29 176 -897 205 -897 -897 -897 -27 71 76 -897 131 -897 76 -897 -897 -897 -897 184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 3.8e+002 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.800000 0.000000 0.600000 0.200000 0.200000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.600000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.400000 0.400000 0.200000 0.000000 0.800000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.400000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][GA][ACG][CA]T[CAG]TG[ATC]G[GTA][GA][ACGT][GC][TA][GC]A[CGA][AG]T -------------------------------------------------------------------------------- Time 1.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 4 llr = 77 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a38:::8:33::a5:::::: pos.-specific C :33::5:a3::::53:::3: probability G :::a:33:53a:::53:a5a matrix T :5::a3:::5:a::38a:3: bits 2.1 * * * * * * * 1.9 * ** * *** ** * 1.7 * ** * *** ** * 1.5 * ** * *** ** * Relative 1.3 * *** ** *** ** * Entropy 1.0 * *** ** **** *** * (27.6 bits) 0.8 * *** ** **** *** * 0.6 * *** *** **** *** * 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel ATAGTCACGTGTAAGTTGGG consensus AC GG AA CCG C sequence C T CG T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 49869 89 4.34e-10 GTATCGTACG AAAGTCGCGAGTACGTTGGG GAGTTGTTGT 6025 1 8.47e-10 . ATCGTCACCTGTAAGTTGCG CAATGCCGAT 47710 403 1.30e-09 ACGCATCCCA ATAGTGACGGGTACCGTGGG AGTATTGGGG 49028 278 3.52e-09 GCACAAACTT ACAGTTACATGTAATTTGTG GTGAATTGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49869 4.3e-10 88_[+3]_392 6025 8.5e-10 [+3]_480 47710 1.3e-09 402_[+3]_78 49028 3.5e-09 277_[+3]_203 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=4 49869 ( 89) AAAGTCGCGAGTACGTTGGG 1 6025 ( 1) ATCGTCACCTGTAAGTTGCG 1 47710 ( 403) ATAGTGACGGGTACCGTGGG 1 49028 ( 278) ACAGTTACATGTAATTTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 3848 bayes= 9.90839 E= 1.0e+003 205 -865 -865 -865 5 3 -865 84 163 3 -865 -865 -865 -865 208 -865 -865 -865 -865 184 -865 103 9 -16 163 -865 9 -865 -865 203 -865 -865 5 3 109 -865 5 -865 9 84 -865 -865 208 -865 -865 -865 -865 184 205 -865 -865 -865 105 103 -865 -865 -865 3 109 -16 -865 -865 9 142 -865 -865 -865 184 -865 -865 208 -865 -865 3 109 -16 -865 -865 208 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 1.0e+003 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.000000 0.500000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.250000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[TAC][AC]GT[CGT][AG]C[GAC][TAG]GTA[AC][GCT][TG]TG[GCT]G -------------------------------------------------------------------------------- Time 1.64 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6025 3.33e-17 [+3(8.47e-10)]_69_[+2(6.39e-10)]_\ 343_[+1(5.25e-10)]_27 47710 6.66e-13 2_[+2(1.77e-11)]_380_[+3(1.30e-09)]_\ 78 49028 4.82e-09 224_[+3(7.27e-05)]_33_\ [+3(3.52e-09)]_78_[+1(2.36e-08)]_104 49142 1.17e-04 184_[+2(2.81e-08)]_296 49869 1.28e-10 88_[+3(4.34e-10)]_146_\ [+1(6.16e-09)]_225 43957 5.05e-05 185_[+1(3.32e-09)]_294 37889 1.61e-08 8_[+2(3.01e-08)]_68_[+1(1.42e-08)]_\ 383 38772 1.51e-09 58_[+2(6.50e-08)]_238_\ [+1(6.68e-10)]_163 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************