******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.5.4 (Release date: ) 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= ../data/oreganno_data/processed_data/regulons_for_one_factor/ftz-f1_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ftz-f1_chr3R_2689754_268 1.0000 15 ftz-f1_chr3R_2510067_251 1.0000 8 ftz-f1_chr2R_7042039_704 1.0000 11 ftz-f1_chr2R_7041814_704 1.0000 11 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme ../data/oreganno_data/processed_data/regulons_for_one_factor/ftz-f1_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 15 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 4 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 45 N= 4 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.200 C 0.300 G 0.300 T 0.200 Background letter frequencies (from dataset with add-one prior applied): A 0.204 C 0.296 G 0.296 T 0.204 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 7 sites = 4 llr = 35 E-value = 1.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::8:::: pos.-specific C 3::aa:: probability G :a::::: matrix T 8:3::aa bits 2.3 ** 2.1 ** 1.8 * **** 1.6 * **** Information 1.4 ******* content 1.1 ******* (12.7 bits) 0.9 ******* 0.7 ******* 0.5 ******* 0.2 ******* 0.0 ------- Multilevel TGACCTT consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- ftz-f1_chr2R_7041814_704 + 3 4.50e-05 GG TGACCTT CG ftz-f1_chr3R_2510067_251 + 1 4.50e-05 . TGACCTT G ftz-f1_chr2R_7042039_704 + 3 8.99e-05 AG TGTCCTT CG ftz-f1_chr3R_2689754_268 - 6 1.55e-04 CGG CGACCTT GAGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ftz-f1_chr2R_7041814_704 4.5e-05 2_[+1]_2 ftz-f1_chr3R_2510067_251 4.5e-05 [+1]_1 ftz-f1_chr2R_7042039_704 9e-05 2_[+1]_2 ftz-f1_chr3R_2689754_268 0.00016 5_[-1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=7 seqs=4 ftz-f1_chr2R_7041814_704 ( 3) TGACCTT 1 ftz-f1_chr3R_2510067_251 ( 1) TGACCTT 1 ftz-f1_chr2R_7042039_704 ( 3) TGTCCTT 1 ftz-f1_chr3R_2689754_268 ( 6) CGACCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 21 bayes= 2.9542 E= 1.4e-003 -865 -24 -865 188 -865 -865 175 -865 188 -865 -865 29 -865 175 -865 -865 -865 175 -865 -865 -865 -865 -865 229 -865 -865 -865 229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 4 E= 1.4e-003 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]G[AT]CCTT -------------------------------------------------------------------------------- Time 0.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ftz-f1_chr3R_2689754_268 2.79e-03 15 ftz-f1_chr3R_2510067_251 1.80e-04 [+1(4.50e-05)]_1 ftz-f1_chr2R_7042039_704 8.99e-04 2_[+1(8.99e-05)]_2 ftz-f1_chr2R_7041814_704 4.50e-04 2_[+1(4.50e-05)]_2 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************