******************************************************************************** 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/Aef1_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Aef1_chr2L_14616265_1461 1.0000 15 Aef1_chrX_9898769_989878 1.0000 18 Aef1_chr2L_14615019_1461 1.0000 24 ******************************************************************************** ******************************************************************************** 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/Aef1_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= 24 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= 57 N= 3 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.281 C 0.219 G 0.219 T 0.281 Background letter frequencies (from dataset with add-one prior applied): A 0.279 C 0.221 G 0.221 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 7 sites = 3 llr = 27 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :aa:7a: pos.-specific C a::a::a probability G ::::::: matrix T ::::3:: bits 2.2 * * * 2.0 * * * 1.7 **** ** 1.5 **** ** Information 1.3 **** ** content 1.1 **** ** (13.0 bits) 0.9 ******* 0.7 ******* 0.4 ******* 0.2 ******* 0.0 ------- Multilevel CAACAAC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- Aef1_chr2L_14615019_1461 + 9 6.54e-05 GACCGCAG CAACAAC ACGATCTTT Aef1_chr2L_14616265_1461 + 4 6.54e-05 AAC CAACAAC TAACG Aef1_chrX_9898769_989878 + 6 1.31e-04 GTGCA CAACTAC AATGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Aef1_chr2L_14615019_1461 6.5e-05 8_[+1]_9 Aef1_chr2L_14616265_1461 6.5e-05 3_[+1]_5 Aef1_chrX_9898769_989878 0.00013 5_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=7 seqs=3 Aef1_chr2L_14615019_1461 ( 9) CAACAAC 1 Aef1_chr2L_14616265_1461 ( 4) CAACAAC 1 Aef1_chrX_9898769_989878 ( 6) CAACTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 39 bayes= 4.06413 E= 3.5e+000 -823 217 -823 -823 184 -823 -823 -823 184 -823 -823 -823 -823 217 -823 -823 126 -823 -823 26 184 -823 -823 -823 -823 217 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 3 E= 3.5e+000 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 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CAAC[AT]AC -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- Aef1_chr2L_14616265_1461 1.18e-03 3_[+1(6.54e-05)]_5 Aef1_chrX_9898769_989878 3.13e-03 18 Aef1_chr2L_14615019_1461 2.35e-03 8_[+1(6.54e-05)]_9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************