******************************************************************************** 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/HLHm5_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ HLHm5_chrX_226541_226558 1.0000 18 HLHm5_chrX_265912_265932 1.0000 21 HLHm5_chr3R_21865771_218 1.0000 15 ******************************************************************************** ******************************************************************************** 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/HLHm5_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= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 3 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 54 N= 3 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.176 C 0.324 G 0.324 T 0.176 Background letter frequencies (from dataset with add-one prior applied): A 0.181 C 0.319 G 0.319 T 0.181 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 3 llr = 38 E-value = 4.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :7::3:::7373: pos.-specific C a:a:::7a:33:: probability G :3:a:a::33::a matrix T ::::7:3::::7: bits 2.5 2.2 2.0 1.7 * ** * * * Information 1.5 * **** * ** content 1.2 ****** ** *** (18.1 bits) 1.0 ********* *** 0.7 ********* *** 0.5 ********* *** 0.2 ************* 0.0 ------------- Multilevel CACGTGCCAAATG consensus G A T GCCA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- HLHm5_chrX_265912_265932 + 2 1.85e-08 G CACGTGTCAAATG CAGATGG HLHm5_chr3R_21865771_218 + 2 8.80e-07 C CACGAGCCACAAG G HLHm5_chrX_226541_226558 - 3 4.95e-06 TGT CGCGTGCCGGCTG CC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HLHm5_chrX_265912_265932 1.9e-08 1_[+1]_7 HLHm5_chr3R_21865771_218 8.8e-07 1_[+1]_1 HLHm5_chrX_226541_226558 5e-06 2_[-1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=3 HLHm5_chrX_265912_265932 ( 2) CACGTGTCAAATG 1 HLHm5_chr3R_21865771_218 ( 2) CACGAGCCACAAG 1 HLHm5_chrX_226541_226558 ( 3) CGCGTGCCGGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 18 bayes= 2.84435 E= 4.2e+000 -823 165 -823 -823 188 -823 6 -823 -823 165 -823 -823 -823 -823 165 -823 88 -823 -823 188 -823 -823 165 -823 -823 106 -823 88 -823 165 -823 -823 188 -823 6 -823 88 6 6 -823 188 6 -823 -823 88 -823 -823 188 -823 -823 165 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 3 E= 4.2e+000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AG]CG[TA]G[CT]C[AG][ACG][AC][TA]G -------------------------------------------------------------------------------- Time 0.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HLHm5_chrX_226541_226558 5.94e-05 2_[-1(4.95e-06)]_3 HLHm5_chrX_265912_265932 3.34e-07 1_[+1(1.85e-08)]_7 HLHm5_chr3R_21865771_218 5.28e-06 1_[+1(8.80e-07)]_1 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************