******************************************************************************** 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/cad_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ cad_chr2L_11455650_11455 1.0000 8 cad_chr3L_20631388_20631 1.0000 11 cad_chr3L_20631445_20631 1.0000 9 cad_chr3L_20631266_20631 1.0000 12 cad_chr2L_11455958_11455 1.0000 27 cad_chr3L_20631297_20631 1.0000 12 cad_chr3R_2689568_268958 1.0000 22 cad_chr2L_11455703_11455 1.0000 16 cad_chr3R_2689641_268966 1.0000 20 cad_chr3L_20631325_20631 1.0000 11 cad_chr3L_20631349_20631 1.0000 14 cad_chr3L_20631235_20631 1.0000 12 cad_chr2L_11455732_11455 1.0000 10 ******************************************************************************** ******************************************************************************** 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/cad_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= 13 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 184 N= 13 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.334 C 0.166 G 0.166 T 0.334 Background letter frequencies (from dataset with add-one prior applied): A 0.332 C 0.168 G 0.168 T 0.332 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 10 llr = 57 E-value = 4.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3178997 pos.-specific C 76:121:: probability G 3122::1: matrix T ::7::::3 bits 2.6 2.3 2.1 1.8 * Information 1.5 * content 1.3 * ** (8.2 bits) 1.0 ** *** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CCTAAAAA consensus GAGGC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- cad_chr3R_2689568_268958 - 2 3.79e-05 TTTATGGTTC CCTAAAAA T cad_chr3L_20631266_20631 + 5 3.79e-05 TTGG CCTAAAAA cad_chr3L_20631349_20631 + 5 2.94e-04 TAAC CATAAAAA TT cad_chr3R_2689641_268966 - 2 2.94e-04 ATCATAAAGA CATAAAAA C cad_chr3L_20631445_20631 + 2 7.18e-04 A GCGGAAAA cad_chr2L_11455703_11455 + 5 2.02e-03 CTTT GCGACAAT TAAG cad_chr2L_11455958_11455 - 19 2.02e-03 C GCTCAAAT ATTGAAAAAT cad_chr3L_20631297_20631 - 5 2.18e-03 . CGTGCAAA CGTG cad_chr3L_20631388_20631 + 4 3.05e-03 GAG CCAAACAA cad_chr3L_20631325_20631 + 2 3.48e-03 T CATAAAGT CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cad_chr3R_2689568_268958 3.8e-05 1_[-1]_13 cad_chr3L_20631266_20631 3.8e-05 4_[+1] cad_chr3L_20631349_20631 0.00029 4_[+1]_2 cad_chr3R_2689641_268966 0.00029 1_[-1]_11 cad_chr3L_20631445_20631 0.00072 1_[+1] cad_chr2L_11455703_11455 0.002 4_[+1]_4 cad_chr2L_11455958_11455 0.002 18_[-1]_1 cad_chr3L_20631297_20631 0.0022 4_[-1] cad_chr3L_20631388_20631 0.003 3_[+1] cad_chr3L_20631325_20631 0.0035 1_[+1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=10 cad_chr3R_2689568_268958 ( 2) CCTAAAAA 1 cad_chr3L_20631266_20631 ( 5) CCTAAAAA 1 cad_chr3L_20631349_20631 ( 5) CATAAAAA 1 cad_chr3R_2689641_268966 ( 2) CATAAAAA 1 cad_chr3L_20631445_20631 ( 2) GCGGAAAA 1 cad_chr2L_11455703_11455 ( 5) GCGACAAT 1 cad_chr2L_11455958_11455 ( 19) GCTCAAAT 1 cad_chr3L_20631297_20631 ( 5) CGTGCAAA 1 cad_chr3L_20631388_20631 ( 4) CCAAACAA 1 cad_chr3L_20631325_20631 ( 2) CATAAAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 93 bayes= 4.07764 E= 4.6e+001 -997 206 84 -997 -15 184 -74 -997 -173 -997 26 107 107 -74 26 -997 127 26 -997 -997 144 -74 -997 -997 144 -997 -74 -997 107 -997 -997 -15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 4.6e+001 0.000000 0.700000 0.300000 0.000000 0.300000 0.600000 0.100000 0.000000 0.100000 0.000000 0.200000 0.700000 0.700000 0.100000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.700000 0.000000 0.000000 0.300000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][CA][TG][AG][AC]AA[AT] -------------------------------------------------------------------------------- Time 0.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cad_chr2L_11455650_11455 5.15e-01 8 cad_chr3L_20631388_20631 2.41e-02 11 cad_chr3L_20631445_20631 2.87e-03 9 cad_chr3L_20631266_20631 3.79e-04 4_[+1(3.79e-05)] cad_chr2L_11455958_11455 7.76e-02 27 cad_chr3L_20631297_20631 2.16e-02 12 cad_chr3R_2689568_268958 1.14e-03 1_[-1(3.79e-05)]_13 cad_chr2L_11455703_11455 3.57e-02 16 cad_chr3R_2689641_268966 7.62e-03 20 cad_chr3L_20631325_20631 2.75e-02 11 cad_chr3L_20631349_20631 4.11e-03 14 cad_chr3L_20631235_20631 8.75e-01 12 cad_chr2L_11455732_11455 7.97e-01 10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************