******************************************************************************** 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/bin_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ bin_chr2L_2445777_244580 1.0000 24 bin_chr2L_2446151_244617 1.0000 25 bin_chr2L_2445847_244586 1.0000 23 bin_chr2R_19816842_19816 1.0000 17 bin_chr2R_19816734_19816 1.0000 20 ******************************************************************************** ******************************************************************************** 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/bin_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= 25 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 5 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 109 N= 5 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.339 C 0.161 G 0.161 T 0.339 Background letter frequencies (from dataset with add-one prior applied): A 0.336 C 0.164 G 0.164 T 0.336 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 5 llr = 48 E-value = 5.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::::22a pos.-specific C 2a24:::::: probability G ::4::a2::: matrix T 8:46a:888: bits 2.6 * * 2.3 * * 2.1 * * 1.8 * * Information 1.6 * ** * content 1.3 * ** * (13.9 bits) 1.0 ** **** * 0.8 ********** 0.5 ********** 0.3 ********** 0.0 ---------- Multilevel TCGTTGTTTA consensus C TC GAA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- bin_chr2L_2445847_244586 + 5 4.18e-06 TGAA TCGCTGGTTA AATATTTAT bin_chr2R_19816734_19816 - 8 1.60e-05 ATT TCTTTGTTTA TTTACGG bin_chr2L_2445777_244580 - 13 1.60e-05 CC TCCTTGTTTA CACTAACTAT bin_chr2R_19816842_19816 + 5 3.25e-05 AGTG CCTTTGTTTA TAG bin_chr2L_2446151_244617 + 3 6.81e-05 AA TCGCTGTAAA TAAATAGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bin_chr2L_2445847_244586 4.2e-06 4_[+1]_9 bin_chr2R_19816734_19816 1.6e-05 7_[-1]_3 bin_chr2L_2445777_244580 1.6e-05 12_[-1]_2 bin_chr2R_19816842_19816 3.2e-05 4_[+1]_3 bin_chr2L_2446151_244617 6.8e-05 2_[+1]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=5 bin_chr2L_2445847_244586 ( 5) TCGCTGGTTA 1 bin_chr2R_19816734_19816 ( 8) TCTTTGTTTA 1 bin_chr2L_2445777_244580 ( 13) TCCTTGTTTA 1 bin_chr2R_19816842_19816 ( 5) CCTTTGTTTA 1 bin_chr2L_2446151_244617 ( 3) TCGCTGTAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 64 bayes= 3.56071 E= 5.3e-001 -897 29 -897 125 -897 261 -897 -897 -897 29 129 25 -897 129 -897 83 -897 -897 -897 157 -897 -897 261 -897 -897 -897 29 125 -75 -897 -897 125 -75 -897 -897 125 157 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5 E= 5.3e-001 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.400000 0.400000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.800000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]C[GTC][TC]TG[TG][TA][TA]A -------------------------------------------------------------------------------- Time 0.04 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bin_chr2L_2445777_244580 4.79e-04 12_[-1(1.60e-05)]_2 bin_chr2L_2446151_244617 2.18e-03 2_[+1(6.81e-05)]_13 bin_chr2L_2445847_244586 1.17e-04 4_[+1(4.18e-06)]_9 bin_chr2R_19816842_19816 5.20e-04 4_[+1(3.25e-05)]_3 bin_chr2R_19816734_19816 3.51e-04 7_[-1(1.60e-05)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************