******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) 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= out_meme_out/meme.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1 1.0000 35 2 1.0000 35 3 1.0000 35 4 1.0000 35 5 1.0000 35 6 1.0000 35 7 1.0000 35 8 1.0000 35 9 1.0000 35 10 1.0000 35 11 1.0000 35 12 1.0000 35 13 1.0000 35 14 1.0000 35 15 1.0000 35 16 1.0000 35 17 1.0000 35 18 1.0000 35 19 1.0000 35 20 1.0000 35 21 1.0000 35 22 1.0000 35 23 1.0000 35 24 1.0000 35 25 1.0000 35 26 1.0000 35 27 1.0000 35 28 1.0000 35 29 1.0000 35 30 1.0000 35 31 1.0000 35 32 1.0000 35 33 1.0000 35 34 1.0000 35 35 1.0000 35 36 1.0000 35 37 1.0000 35 38 1.0000 35 39 1.0000 35 40 1.0000 35 41 1.0000 35 42 1.0000 35 43 1.0000 35 44 1.0000 35 45 1.0000 35 46 1.0000 35 47 1.0000 35 48 1.0000 35 49 1.0000 35 50 1.0000 35 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme out_meme_out/meme.fasta -mod zoops -prior dirichlet -nostatus -dna -oc out_meme_out/ model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 35 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 50 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= 1750 N= 50 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.233 C 0.279 G 0.333 T 0.155 Background letter frequencies (from dataset with add-one prior applied): A 0.233 C 0.279 G 0.332 T 0.156 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 14 sites = 8 llr = 92 E-value = 3.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 6:3::::84:5449 pos.-specific C 4:13::4:51:3:: probability G :::::93119535: matrix T :a68a141:::111 bits 2.7 * * 2.4 * * 2.1 * * 1.9 * * Relative 1.6 * ** * Entropy 1.3 * ** * (16.6 bits) 1.1 ****** * * * 0.8 ****** * ** * 0.5 *********** ** 0.3 *********** ** 0.0 -------------- Multilevel ATTTTGCACGAAGA consensus C AC T A GCA sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 31 5 2.54e-07 CCCT ATTTTGGAAGGCAA GAAAAGGTTG 46 6 5.45e-07 CCCTC ATCTTGCACGAAAA AGGGAAAGGG 32 20 5.45e-07 GGATTGGGAC ATTTTGGAGGAAAA TG 5 15 1.34e-06 GACTTCACCG ATATTTTAAGAGGA TGCAGCA 50 18 1.65e-06 CCGACCCGGG CTTCTGTAAGGTGA CGCC 26 15 3.38e-06 GGATACGATA CTTTTGCACCGGGA GTGGTAC 8 16 8.35e-06 CTACACCCGG ATATTGCGCGACTA TTTCGC 44 6 1.14e-05 CTTGG CTTCTGTTCGGAGT TCAGGAGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31 2.5e-07 4_[1]_17 46 5.5e-07 5_[1]_16 32 5.5e-07 19_[1]_2 5 1.3e-06 14_[1]_7 50 1.7e-06 17_[1]_4 26 3.4e-06 14_[1]_7 8 8.3e-06 15_[1]_6 44 1.1e-05 5_[1]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=8 31 ( 5) ATTTTGGAAGGCAA 1 46 ( 6) ATCTTGCACGAAAA 1 32 ( 20) ATTTTGGAGGAAAA 1 5 ( 15) ATATTTTAAGAGGA 1 50 ( 18) CTTCTGTAAGGTGA 1 26 ( 15) CTTTTGCACCGGGA 1 8 ( 16) ATATTGCGCGACTA 1 44 ( 6) CTTCTGTTCGGAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1100 bayes= 7.09276 E= 3.5e-001 142 43 -965 -965 -965 -965 -965 268 10 -116 -965 200 -965 -16 -965 227 -965 -965 -965 268 -965 -965 140 -32 -965 43 -41 127 168 -965 -141 -32 68 84 -141 -965 -965 -116 140 -965 110 -965 59 -965 68 -16 -41 -32 68 -965 59 -32 191 -965 -965 -32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 3.5e-001 0.625000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.125000 0.000000 0.625000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.375000 0.250000 0.375000 0.750000 0.000000 0.125000 0.125000 0.375000 0.500000 0.125000 0.000000 0.000000 0.125000 0.875000 0.000000 0.500000 0.000000 0.500000 0.000000 0.375000 0.250000 0.250000 0.125000 0.375000 0.000000 0.500000 0.125000 0.875000 0.000000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC]T[TA][TC]TG[CTG]A[CA]G[AG][ACG][GA]A -------------------------------------------------------------------------------- Time 0.94 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 1.07e-01 35 2 2.28e-01 35 3 2.01e-01 35 4 4.97e-01 35 5 2.96e-05 14_[1(1.34e-06)]_7 6 4.51e-01 35 7 2.09e-01 35 8 1.84e-04 15_[1(8.35e-06)]_6 9 1.93e-01 35 10 4.97e-01 35 11 7.41e-01 35 12 6.79e-01 35 13 3.59e-01 35 14 6.74e-01 35 15 4.58e-01 35 16 7.62e-01 35 17 8.02e-02 35 18 8.83e-01 35 19 4.00e-02 35 20 2.96e-01 35 21 1.16e-01 35 22 8.87e-01 35 23 9.16e-01 35 24 8.28e-01 35 25 4.43e-01 35 26 7.45e-05 14_[1(3.38e-06)]_7 27 3.59e-01 35 28 2.09e-02 35 29 5.91e-01 35 30 2.06e-01 35 31 5.59e-06 4_[1(2.54e-07)]_17 32 1.20e-05 19_[1(5.45e-07)]_2 33 7.19e-01 35 34 8.65e-01 35 35 9.41e-01 35 36 8.51e-01 35 37 7.48e-01 35 38 8.01e-01 35 39 6.79e-01 35 40 8.37e-01 35 41 6.84e-01 35 42 6.10e-01 35 43 9.78e-01 35 44 2.51e-04 5_[1(1.14e-05)]_16 45 8.96e-01 35 46 1.20e-05 5_[1(5.45e-07)]_16 47 4.43e-01 35 48 1.57e-01 35 49 1.66e-01 35 50 3.63e-05 17_[1(1.65e-06)]_4 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************