******************************************************************************** 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/tin_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ tin_chr2R_19812026_19812 1.0000 16 tin_chr2R_5497333_549733 1.0000 7 tin_chr2R_5447302_544731 1.0000 9 tin_chr2R_5497461_549746 1.0000 7 tin_chr3R_17209536_17209 1.0000 8 tin_chr2R_19811989_19812 1.0000 16 tin_chr2R_5447129_544713 1.0000 9 tin_chr3R_17209345_17209 1.0000 8 tin_chr2R_5497516_549752 1.0000 7 tin_chr2R_19816868_19816 1.0000 18 tin_chr2R_5497350_549735 1.0000 7 ******************************************************************************** ******************************************************************************** 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/tin_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= 18 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 11 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 112 N= 11 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.250 C 0.250 G 0.250 T 0.250 Background letter frequencies (from dataset with add-one prior applied): A 0.250 C 0.250 G 0.250 T 0.250 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 11 llr = 76 E-value = 5.7e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 9:::29 pos.-specific C 1a::1: probability G ::::71 matrix T ::aa:: bits 2.0 *** 1.8 *** 1.6 **** * 1.4 **** * Information 1.2 **** * content 1.0 ****** (10.0 bits) 0.8 ****** 0.6 ****** 0.4 ****** 0.2 ****** 0.0 ------ Multilevel ACTTGA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ tin_chr2R_19816868_19816 - 1 2.44e-04 TGGCACTTGA ACTTGA tin_chr2R_5497516_549752 + 2 2.44e-04 C ACTTGA tin_chr3R_17209345_17209 - 1 2.44e-04 CC ACTTGA tin_chr2R_5447129_544713 - 2 2.44e-04 CC ACTTGA G tin_chr2R_19811989_19812 + 7 2.44e-04 TGAAGC ACTTGA GGAG tin_chr3R_17209536_17209 - 1 2.44e-04 CC ACTTGA tin_chr2R_5447302_544731 + 3 2.44e-04 CC ACTTGA G tin_chr2R_5497350_549735 + 2 4.88e-04 C ACTTAA tin_chr2R_5497333_549733 + 1 7.32e-04 . ACTTCA C tin_chr2R_5497461_549746 + 2 1.22e-03 C CCTTGA tin_chr2R_19812026_19812 + 8 1.71e-03 CCTCCCC ACTTAG GCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- tin_chr2R_19816868_19816 0.00024 [-1]_12 tin_chr2R_5497516_549752 0.00024 1_[+1] tin_chr3R_17209345_17209 0.00024 [-1]_2 tin_chr2R_5447129_544713 0.00024 1_[-1]_2 tin_chr2R_19811989_19812 0.00024 6_[+1]_4 tin_chr3R_17209536_17209 0.00024 [-1]_2 tin_chr2R_5447302_544731 0.00024 2_[+1]_1 tin_chr2R_5497350_549735 0.00049 1_[+1] tin_chr2R_5497333_549733 0.00073 [+1]_1 tin_chr2R_5497461_549746 0.0012 1_[+1] tin_chr2R_19812026_19812 0.0017 7_[+1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=11 tin_chr2R_19816868_19816 ( 1) ACTTGA 1 tin_chr2R_5497516_549752 ( 2) ACTTGA 1 tin_chr3R_17209345_17209 ( 1) ACTTGA 1 tin_chr2R_5447129_544713 ( 2) ACTTGA 1 tin_chr2R_19811989_19812 ( 7) ACTTGA 1 tin_chr3R_17209536_17209 ( 1) ACTTGA 1 tin_chr2R_5447302_544731 ( 3) ACTTGA 1 tin_chr2R_5497350_549735 ( 2) ACTTAA 1 tin_chr2R_5497333_549733 ( 1) ACTTCA 1 tin_chr2R_5497461_549746 ( 2) CCTTGA 1 tin_chr2R_19812026_19812 ( 8) ACTTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 57 bayes= 2.06413 E= 5.7e-013 186 -146 -1010 -1010 -1010 200 -1010 -1010 -1010 -1010 -1010 200 -1010 -1010 -1010 200 -46 -146 154 -1010 186 -1010 -146 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 11 E= 5.7e-013 0.909091 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.181818 0.090909 0.727273 0.000000 0.909091 0.000000 0.090909 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- ACTTGA -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- tin_chr2R_19812026_19812 3.69e-02 16 tin_chr2R_5497333_549733 2.93e-03 7 tin_chr2R_5447302_544731 1.95e-03 9 tin_chr2R_5497461_549746 4.87e-03 7 tin_chr3R_17209536_17209 1.46e-03 8 tin_chr2R_19811989_19812 5.36e-03 16 tin_chr2R_5447129_544713 1.95e-03 9 tin_chr3R_17209345_17209 1.46e-03 8 tin_chr2R_5497516_549752 9.77e-04 7 tin_chr2R_19816868_19816 6.33e-03 18 tin_chr2R_5497350_549735 1.95e-03 7 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************