******************************************************************************** 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/313/313.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 16987 1.0000 500 45799 1.0000 500 49128 1.0000 500 49510 1.0000 500 49718 1.0000 500 35749 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/313/313.seqs.fa -oc motifs/313 -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= 6 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= 3000 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.283 C 0.241 G 0.217 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.283 C 0.241 G 0.217 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 18 sites = 6 llr = 95 E-value = 1.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::3::::523:5::88 pos.-specific C 232:22::2:8::5a:2: probability G ::7::5a:53:73::a:: matrix T 872a53:a32::7::::2 bits 2.2 * * 2.0 * ** ** 1.8 * ** ** 1.5 * ** ** Relative 1.3 * * ** * *** Entropy 1.1 ** * ** *** **** (22.8 bits) 0.9 **** ** ******** 0.7 **** **** ******** 0.4 ****************** 0.2 ****************** 0.0 ------------------ Multilevel TTGTTGGTGACGTACGAA consensus C AT TG AGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 16987 457 2.19e-09 TCGAGGAATA TTGTCGGTTGCGTACGAA CATCGCCTGT 45799 96 2.74e-09 GCTAGCTTTC CTGTTGGTGACGGCCGAA AAAGAAAAAA 49718 454 5.01e-09 ACAGCGTCCA TTGTACGTTACGTACGAA CGGTTGAAAA 49128 206 9.89e-08 TCGTCGTTCT TCGTTGGTGGAATCCGAT TCTTCTCGAT 49510 407 1.11e-07 AACAATCCAG TCCTTTGTGTCGTCCGCA AATTTTGTGA 35749 282 1.41e-07 CAGTATAGAA TTTTATGTCACAGACGAA AAACCTACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16987 2.2e-09 456_[+1]_26 45799 2.7e-09 95_[+1]_387 49718 5e-09 453_[+1]_29 49128 9.9e-08 205_[+1]_277 49510 1.1e-07 406_[+1]_76 35749 1.4e-07 281_[+1]_201 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=18 seqs=6 16987 ( 457) TTGTCGGTTGCGTACGAA 1 45799 ( 96) CTGTTGGTGACGGCCGAA 1 49718 ( 454) TTGTACGTTACGTACGAA 1 49128 ( 206) TCGTTGGTGGAATCCGAT 1 49510 ( 407) TCCTTTGTGTCGTCCGCA 1 35749 ( 282) TTTTATGTCACAGACGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 2898 bayes= 8.91289 E= 1.0e+000 -923 -53 -923 168 -923 47 -923 136 -923 -53 162 -64 -923 -923 -923 195 24 -53 -923 95 -923 -53 120 36 -923 -923 220 -923 -923 -923 -923 195 -923 -53 120 36 82 -923 62 -64 -76 179 -923 -923 24 -923 162 -923 -923 -923 62 136 82 105 -923 -923 -923 205 -923 -923 -923 -923 220 -923 156 -53 -923 -923 156 -923 -923 -64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 6 E= 1.0e+000 0.000000 0.166667 0.000000 0.833333 0.000000 0.333333 0.000000 0.666667 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.000000 1.000000 0.333333 0.166667 0.000000 0.500000 0.000000 0.166667 0.500000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.500000 0.333333 0.500000 0.000000 0.333333 0.166667 0.166667 0.833333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[TC]GT[TA][GT]GT[GT][AG]C[GA][TG][AC]CGAA -------------------------------------------------------------------------------- Time 0.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 4 llr = 81 E-value = 2.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::5:a8:::5:835:::: pos.-specific C ::3:33::::5::3:5::a: probability G :a8838:::::3a:3:aa:8 matrix T a::3:::3aa53::5::::3 bits 2.2 * * ** 2.0 ** ** * *** 1.8 ** * ** * *** 1.5 ** * ** * *** Relative 1.3 **** ** ** * **** Entropy 1.1 **** ****** ** **** (29.3 bits) 0.9 **** ****** ** ***** 0.7 **** ****** ** ***** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TGGGAGAATTCAGATAGGCG consensus CTCC T TG CAC T sequence G T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 49128 244 3.54e-11 TGGACTCTAC TGGGAGAATTTGGAACGGCG GATCGTCGCA 45799 26 1.75e-10 TTGTGAGCCT TGGGCGAATTCAGCGAGGCG TGAAATTAGC 35749 133 8.99e-10 AGCTGCGCCA TGCTGGAATTTTGATCGGCG AGTTCGAAGC 16987 9 1.02e-09 CTTCTTTG TGGGACATTTCAGATAGGCT CAATTTGAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49128 3.5e-11 243_[+2]_237 45799 1.8e-10 25_[+2]_455 35749 9e-10 132_[+2]_348 16987 1e-09 8_[+2]_472 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=4 49128 ( 244) TGGGAGAATTTGGAACGGCG 1 45799 ( 26) TGGGCGAATTCAGCGAGGCG 1 35749 ( 133) TGCTGGAATTTTGATCGGCG 1 16987 ( 9) TGGGACATTTCAGATAGGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2886 bayes= 9.49285 E= 2.6e+000 -865 -865 -865 194 -865 -865 220 -865 -865 5 178 -865 -865 -865 178 -5 82 5 20 -865 -865 5 178 -865 182 -865 -865 -865 141 -865 -865 -5 -865 -865 -865 194 -865 -865 -865 194 -865 105 -865 95 82 -865 20 -5 -865 -865 220 -865 141 5 -865 -865 -18 -865 20 95 82 105 -865 -865 -865 -865 220 -865 -865 -865 220 -865 -865 205 -865 -865 -865 -865 178 -5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 2.6e+000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.500000 0.250000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.500000 0.000000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.000000 0.250000 0.500000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[GC][GT][ACG][GC]A[AT]TT[CT][AGT]G[AC][TAG][AC]GGC[GT] -------------------------------------------------------------------------------- Time 0.74 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 94 E-value = 8.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 8:2:3:7:::8:223:52:: pos.-specific C :722:8:2:a25:327:3:a probability G :::82:37:::5:3:::3:: matrix T 237:52:2a:::825352a: bits 2.2 2.0 ** ** 1.8 ** ** 1.5 * ** ** Relative 1.3 * * *** * ** Entropy 1.1 ** * ** ***** * ** (22.6 bits) 0.9 ** * ******** ** ** 0.7 **** ******** ** ** 0.4 ************* *** ** 0.2 ******************** 0.0 -------------------- Multilevel ACTGTCAGTCACTCTCACTC consensus T A G G GATTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 16987 290 3.42e-10 TCTCACTGTC ACTGTCAGTCAGTGACAATC CCAATACCGA 35749 176 1.28e-09 CGAAAAGATA ACTGTCGTTCACTGTCAGTC CCAGAAGATG 49128 381 6.65e-09 CATTCCCATA ATAGTCAGTCAGTCTTTCTC CAACAACTGA 45799 289 1.67e-08 ATGAGATTCC ATTCACAGTCACTTTCTGTC AAGATAAGTA 49510 456 3.48e-07 CCATCCTTCC ACCGATACTCACACACACTC ATACACACAT 49718 112 4.59e-07 TCTGTGGGCG TCTGGCGGTCCGTACTTTTC GAATAAGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16987 3.4e-10 289_[+3]_191 35749 1.3e-09 175_[+3]_305 49128 6.6e-09 380_[+3]_100 45799 1.7e-08 288_[+3]_192 49510 3.5e-07 455_[+3]_25 49718 4.6e-07 111_[+3]_369 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 16987 ( 290) ACTGTCAGTCAGTGACAATC 1 35749 ( 176) ACTGTCGTTCACTGTCAGTC 1 49128 ( 381) ATAGTCAGTCAGTCTTTCTC 1 45799 ( 289) ATTCACAGTCACTTTCTGTC 1 49510 ( 456) ACCGATACTCACACACACTC 1 49718 ( 112) TCTGGCGGTCCGTACTTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2886 bayes= 8.90689 E= 8.3e+001 156 -923 -923 -64 -923 147 -923 36 -76 -53 -923 136 -923 -53 194 -923 24 -923 -38 95 -923 179 -923 -64 124 -923 62 -923 -923 -53 162 -64 -923 -923 -923 195 -923 205 -923 -923 156 -53 -923 -923 -923 105 120 -923 -76 -923 -923 168 -76 47 62 -64 24 -53 -923 95 -923 147 -923 36 82 -923 -923 95 -76 47 62 -64 -923 -923 -923 195 -923 205 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 8.3e+001 0.833333 0.000000 0.000000 0.166667 0.000000 0.666667 0.000000 0.333333 0.166667 0.166667 0.000000 0.666667 0.000000 0.166667 0.833333 0.000000 0.333333 0.000000 0.166667 0.500000 0.000000 0.833333 0.000000 0.166667 0.666667 0.000000 0.333333 0.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.333333 0.333333 0.166667 0.333333 0.166667 0.000000 0.500000 0.000000 0.666667 0.000000 0.333333 0.500000 0.000000 0.000000 0.500000 0.166667 0.333333 0.333333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[CT]TG[TA]C[AG]GTCA[CG]T[CG][TA][CT][AT][CG]TC -------------------------------------------------------------------------------- Time 1.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16987 8.63e-17 8_[+2(1.02e-09)]_261_[+3(3.42e-10)]_\ 147_[+1(2.19e-09)]_26 45799 8.11e-16 25_[+2(1.75e-10)]_50_[+1(2.74e-09)]_\ 175_[+3(1.67e-08)]_192 49128 2.24e-15 205_[+1(9.89e-08)]_20_\ [+2(3.54e-11)]_117_[+3(6.65e-09)]_100 49510 1.33e-06 406_[+1(1.11e-07)]_31_\ [+3(3.48e-07)]_25 49718 1.11e-07 111_[+3(4.59e-07)]_322_\ [+1(5.01e-09)]_29 35749 1.42e-14 132_[+2(8.99e-10)]_23_\ [+3(1.28e-09)]_86_[+1(1.41e-07)]_201 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************