******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.5.7 (Release date: 2007-12-17 16:56:19 -0800 (Mon, 17 Dec 2007)) 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= test.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ SEQ1; 1.0000 200 SEQ2; 1.0000 200 SEQ3; 1.0000 200 SEQ4; 1.0000 200 SEQ5; 1.0000 200 SEQ6; 1.0000 200 SEQ7; 1.0000 200 SEQ8; 1.0000 200 SEQ9; 1.0000 200 SEQ10; 1.0000 200 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme test.fa -dna -w 10 -dir /home/bartek/MetaMotif/meme model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 10 maxw= 10 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 10 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 2000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.235 G 0.261 T 0.249 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.236 G 0.260 T 0.249 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 10 llr = 140 E-value = 1.1e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::aa::::a pos.-specific C a:a:::a::: probability G :::::::a:: matrix T :a:::a::a: bits 2.1 *** ** * 1.9 ********** 1.7 ********** 1.5 ********** Information 1.3 ********** content 1.0 ********** (20.1 bits) 0.8 ********** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel CTCAATCGTA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------- SEQ10; 3 8.71e-07 TT CTCAATCGTA GAGTATGCTT SEQ9; 93 8.71e-07 CGCCTAGAAA CTCAATCGTA GAGTATCACG SEQ8; 172 8.71e-07 CCCGGAGTAT CTCAATCGTA GATGAATACC SEQ7; 177 8.71e-07 AAGTCTTTGA CTCAATCGTA GACCCAACAC SEQ6; 105 8.71e-07 GTCAGCCGGT CTCAATCGTA GATCAGAGGC SEQ5; 185 8.71e-07 ACGGGCAAGC CTCAATCGTA GAGGAT SEQ4; 173 8.71e-07 GTTCGAGAGC CTCAATCGTA GATAACCTCT SEQ3; 112 8.71e-07 GTTATATTGG CTCAATCGTA GATGAAACCA SEQ2; 172 8.71e-07 AAGCGTCGTG CTCAATCGTA GATAACAGAG SEQ1; 52 8.71e-07 CTTTACTCGG CTCAATCGTA GAGGCGGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SEQ10; 8.7e-07 2_[1]_188 SEQ9; 8.7e-07 92_[1]_98 SEQ8; 8.7e-07 171_[1]_19 SEQ7; 8.7e-07 176_[1]_14 SEQ6; 8.7e-07 104_[1]_86 SEQ5; 8.7e-07 184_[1]_6 SEQ4; 8.7e-07 172_[1]_18 SEQ3; 8.7e-07 111_[1]_79 SEQ2; 8.7e-07 171_[1]_19 SEQ1; 8.7e-07 51_[1]_139 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=10 SEQ10; ( 3) CTCAATCGTA 1 SEQ9; ( 93) CTCAATCGTA 1 SEQ8; ( 172) CTCAATCGTA 1 SEQ7; ( 177) CTCAATCGTA 1 SEQ6; ( 105) CTCAATCGTA 1 SEQ5; ( 185) CTCAATCGTA 1 SEQ4; ( 173) CTCAATCGTA 1 SEQ3; ( 112) CTCAATCGTA 1 SEQ2; ( 172) CTCAATCGTA 1 SEQ1; ( 52) CTCAATCGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1910 bayes= 8.51691 E= 1.1e-022 -997 208 -997 -997 -997 -997 -997 200 -997 208 -997 -997 197 -997 -997 -997 197 -997 -997 -997 -997 -997 -997 200 -997 208 -997 -997 -997 -997 194 -997 -997 -997 -997 200 197 -997 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 10 E= 1.1e-022 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CTCAATCGTA -------------------------------------------------------------------------------- Time 0.26 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SEQ1; 1.66e-04 51_[1(8.71e-07)]_139 SEQ2; 1.66e-04 171_[1(8.71e-07)]_19 SEQ3; 1.66e-04 111_[1(8.71e-07)]_79 SEQ4; 1.66e-04 172_[1(8.71e-07)]_18 SEQ5; 1.66e-04 184_[1(8.71e-07)]_6 SEQ6; 1.66e-04 104_[1(8.71e-07)]_86 SEQ7; 1.66e-04 176_[1(8.71e-07)]_14 SEQ8; 1.66e-04 171_[1(8.71e-07)]_19 SEQ9; 1.66e-04 92_[1(8.71e-07)]_98 SEQ10; 1.66e-04 2_[1(8.71e-07)]_188 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: pc-arendt9 ********************************************************************************