******************************************************************************** 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/gt_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ gt_chr2R_20732895_207329 1.0000 16 gt_chr3L_20630799_206308 1.0000 15 gt_chr3L_20630776_206307 1.0000 12 gt_chr2R_5489745_5489789 1.0000 45 gt_chr3R_12636939_126369 1.0000 23 gt_chr2R_5490014_5490036 1.0000 23 gt_chr2R_20730906_207309 1.0000 16 gt_chr2R_5489682_5489707 1.0000 26 ******************************************************************************** ******************************************************************************** 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/gt_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= 8 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 176 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.338 C 0.162 G 0.162 T 0.338 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 = 8 llr = 56 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:6::8:::6 pos.-specific C :::::36:4: probability G :13:6:35:: matrix T 691a4:1564 bits 2.6 2.3 2.1 1.8 Information 1.6 * content 1.3 ** * (10.1 bits) 1.0 * ****** 0.8 * ****** 0.5 ********** 0.3 ********** 0.0 ---------- Multilevel TTATGACGTA consensus A G TCGTCT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- gt_chr2R_20730906_207309 - 6 1.04e-06 T TTATGACGCA AGAAT gt_chr2R_5490014_5490036 - 2 7.40e-05 TTATGTGTTT TTATGACTTT C gt_chr3R_12636939_126369 - 2 1.54e-04 ACCTTTCATA ATATTACGTA A gt_chr2R_20732895_207329 - 6 1.83e-04 A ATGTTACGTA AAATT gt_chr2R_5489682_5489707 + 6 4.24e-04 CGAGA TTATTAGTCA ATTGCAGTTG gt_chr3L_20630776_206307 - 3 4.24e-04 . TTGTGCGTTT TT gt_chr3L_20630799_206308 - 2 5.18e-04 TGCT TTTTGACTTT T gt_chr2R_5489745_5489789 - 9 1.21e-03 CGATTGTTCA AGATGCTGCA ATAAAGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- gt_chr2R_20730906_207309 1e-06 5_[-1]_1 gt_chr2R_5490014_5490036 7.4e-05 1_[-1]_12 gt_chr3R_12636939_126369 0.00015 1_[-1]_12 gt_chr2R_20732895_207329 0.00018 5_[-1]_1 gt_chr2R_5489682_5489707 0.00042 5_[+1]_11 gt_chr3L_20630776_206307 0.00042 2_[-1] gt_chr3L_20630799_206308 0.00052 1_[-1]_4 gt_chr2R_5489745_5489789 0.0012 8_[-1]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=8 gt_chr2R_20730906_207309 ( 6) TTATGACGCA 1 gt_chr2R_5490014_5490036 ( 2) TTATGACTTT 1 gt_chr3R_12636939_126369 ( 2) ATATTACGTA 1 gt_chr2R_20732895_207329 ( 6) ATGTTACGTA 1 gt_chr2R_5489682_5489707 ( 6) TTATTAGTCA 1 gt_chr3L_20630776_206307 ( 3) TTGTGCGTTT 1 gt_chr3L_20630799_206308 ( 2) TTTTGACTTT 1 gt_chr2R_5489745_5489789 ( 9) AGATGCTGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 104 bayes= 3.58496 E= 1.1e+001 16 -965 -965 89 -965 -965 -39 138 89 -965 61 -142 -965 -965 -965 157 -965 -965 193 16 116 61 -965 -965 -965 193 61 -142 -965 -965 161 57 -965 119 -965 89 89 -965 -965 16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 8 E= 1.1e+001 0.375000 0.000000 0.000000 0.625000 0.000000 0.000000 0.125000 0.875000 0.625000 0.000000 0.250000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.625000 0.375000 0.750000 0.250000 0.000000 0.000000 0.000000 0.625000 0.250000 0.125000 0.000000 0.000000 0.500000 0.500000 0.000000 0.375000 0.000000 0.625000 0.625000 0.000000 0.000000 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA]T[AG]T[GT][AC][CG][GT][TC][AT] -------------------------------------------------------------------------------- Time 0.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- gt_chr2R_20732895_207329 2.56e-03 16 gt_chr3L_20630799_206308 6.20e-03 15 gt_chr3L_20630776_206307 2.54e-03 12 gt_chr2R_5489745_5489789 8.38e-02 45 gt_chr3R_12636939_126369 4.31e-03 23 gt_chr2R_5490014_5490036 2.07e-03 1_[-1(7.40e-05)]_12 gt_chr2R_20730906_207309 1.46e-05 5_[-1(1.04e-06)]_1 gt_chr2R_5489682_5489707 1.43e-02 26 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************