******************************************************************************** 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= upstream.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ NC_046965.1 1.0000 553 NC_046965.2 1.0000 100 NC_046965.3 1.0000 100 NC_046965.4 1.0000 100 NC_046965.5 1.0000 1100 NC_046965.6 1.0000 100 NC_046965.7 1.0000 100 NC_046965.8 1.0000 100 NC_046965.9 1.0000 100 NC_046965.10 1.0000 100 NC_046965.11 1.0000 99 NC_046965.12 1.0000 100 NC_046965.13 1.0000 100 NC_046965.14 1.0000 109 NC_046965.15 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme upstream.fasta -oc result -dna -mod zoops -nmotifs 1 -minw 6 -maxw 50 -minsites 2 model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 15 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= 2961 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.187 G 0.208 T 0.333 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.187 G 0.208 T 0.333 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 12 sites = 8 llr = 105 E-value = 1.2e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3::a91a9a81: pos.-specific C 8::::9:1::81 probability G ::::1::::3:9 matrix T :aa:::::::1: bits 2.4 2.2 1.9 * * * 1.7 *** ** * * Relative 1.5 ********* * Entropy 1.2 ************ (19.0 bits) 1.0 ************ 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel CTTAACAAAACG consensus A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ NC_046965.11 87 6.11e-08 GTAGTGAGCC CTTAACAAAACG G NC_046965.5 961 6.11e-08 TTATTTGAAT CTTAACAAAACG CATGTTTTAT NC_046965.4 88 6.11e-08 TTATTTGAAT CTTAACAAAACG C NC_046965.1 64 6.11e-08 AGAACCTTTT CTTAACAAAACG GACTTATAGT NC_046965.9 89 1.97e-07 CTTTGGCAGA ATTAACAAAACG NC_046965.8 86 2.62e-06 TTAAAGGAGT CTTAACAAAATC GGC NC_046965.2 9 4.41e-06 TTGTTACT CTTAAAAAAGAG CTTCAATCGG NC_046965.3 15 5.17e-06 GCCTAATTCC ATTAGCACAGCG TTGCAGTAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NC_046965.11 6.1e-08 86_[1]_1 NC_046965.5 6.1e-08 960_[1]_128 NC_046965.4 6.1e-08 87_[1]_1 NC_046965.1 6.1e-08 63_[1]_478 NC_046965.9 2e-07 88_[1] NC_046965.8 2.6e-06 85_[1]_3 NC_046965.2 4.4e-06 8_[1]_80 NC_046965.3 5.2e-06 14_[1]_74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=8 NC_046965.11 ( 87) CTTAACAAAACG 1 NC_046965.5 ( 961) CTTAACAAAACG 1 NC_046965.4 ( 88) CTTAACAAAACG 1 NC_046965.1 ( 64) CTTAACAAAACG 1 NC_046965.9 ( 89) ATTAACAAAACG 1 NC_046965.8 ( 86) CTTAACAAAATC 1 NC_046965.2 ( 9) CTTAAAAAAGAG 1 NC_046965.3 ( 15) ATTAGCACAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 2796 bayes= 8.44501 E= 1.2e-007 -12 200 -965 -965 -965 -965 -965 159 -965 -965 -965 159 188 -965 -965 -965 169 -965 -74 -965 -112 223 -965 -965 188 -965 -965 -965 169 -58 -965 -965 188 -965 -965 -965 146 -965 26 -965 -112 200 -965 -141 -965 -58 207 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 1.2e-007 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.125000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.125000 0.750000 0.000000 0.125000 0.000000 0.125000 0.875000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]TTAACAAA[AG]CG -------------------------------------------------------------------------------- Time 2.04 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NC_046965.1 3.31e-05 63_[1(6.11e-08)]_478 NC_046965.2 3.93e-04 8_[1(4.41e-06)]_80 NC_046965.3 4.61e-04 14_[1(5.17e-06)]_74 NC_046965.4 5.44e-06 87_[1(6.11e-08)]_1 NC_046965.5 6.65e-05 717_[1(5.17e-06)]_231_[1(6.11e-08)]_128 NC_046965.6 2.51e-01 100 NC_046965.7 3.64e-01 100 NC_046965.8 2.33e-04 85_[1(2.62e-06)]_3 NC_046965.9 1.75e-05 88_[1(1.97e-07)] NC_046965.10 9.40e-01 100 NC_046965.11 5.37e-06 86_[1(6.11e-08)]_1 NC_046965.12 3.72e-01 100 NC_046965.13 3.51e-01 100 NC_046965.14 4.08e-01 109 NC_046965.15 5.10e-02 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: kodomo ********************************************************************************