******************************************************************************** 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/tll_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ tll_chr2R_20730463_20730 1.0000 10 tll_chr3L_20630716_20630 1.0000 21 tll_chr2R_20730905_20730 1.0000 9 tll_chr3L_8639774_863978 1.0000 13 tll_chr3R_4527314_452732 1.0000 13 tll_chr3L_8639157_863916 1.0000 13 tll_chr3L_20630429_20630 1.0000 26 tll_chr3L_20630598_20630 1.0000 17 tll_chr3R_4527236_452725 1.0000 20 tll_chr3R_12526878_12526 1.0000 25 tll_chr2R_20730564_20730 1.0000 12 tll_chr3L_20630517_20630 1.0000 17 tll_chr3L_8639260_863927 1.0000 15 tll_chr2R_20730328_20730 1.0000 16 tll_chr3R_9720721_972073 1.0000 15 tll_chr3R_4527002_452702 1.0000 21 tll_chr3R_4527523_452754 1.0000 20 tll_chr3R_12599144_12599 1.0000 14 tll_chr3R_12526966_12526 1.0000 27 tll_chr3R_12527089_12527 1.0000 18 tll_chr3R_4527487_452750 1.0000 17 tll_chr3R_4526654_452668 1.0000 34 tll_chr3L_8640905_864092 1.0000 18 tll_chr3L_8639319_863933 1.0000 15 tll_chr3R_12599286_12599 1.0000 18 tll_chr3L_20630381_20630 1.0000 17 tll_chr3R_4527306_452731 1.0000 6 tll_chr2R_20730532_20730 1.0000 10 tll_chr2R_20730810_20730 1.0000 19 tll_chr3R_4527125_452715 1.0000 28 tll_chr3L_20630476_20630 1.0000 16 tll_chr3R_4526813_452683 1.0000 19 tll_chr3L_8639597_863960 1.0000 13 tll_chr3R_9720621_972063 1.0000 13 tll_chr3L_8641202_864123 1.0000 29 tll_chr3L_20630701_20630 1.0000 14 tll_chr2R_20730481_20730 1.0000 8 ******************************************************************************** ******************************************************************************** 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/tll_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= 37 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 636 N= 37 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.305 C 0.195 G 0.195 T 0.305 Background letter frequencies (from dataset with add-one prior applied): A 0.305 C 0.195 G 0.195 T 0.305 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 22 llr = 144 E-value = 4.1e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1:28:::1 pos.-specific C 2::1a123 probability G ::8::::: matrix T 7a:::886 bits 2.4 2.1 * 1.9 * 1.6 * * Information 1.4 ** * content 1.2 ** * * (9.4 bits) 0.9 ****** 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTGACTTT consensus A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- tll_chr3L_8641202_864123 - 16 3.05e-05 TCGCAT TTGACTTT TTGGCTTTTC tll_chr3L_20630381_20630 - 5 3.05e-05 GGAAG TTGACTTT TAAA tll_chr3L_20630598_20630 + 3 3.05e-05 CC TTGACTTT TTCACTC tll_chr3L_20630716_20630 + 11 3.05e-05 GATTTTCCAT TTGACTTT CAT tll_chr2R_20730810_20730 - 9 5.01e-05 AAT TTGACTTC TTAATTGC tll_chr3R_9720721_972073 + 5 6.96e-05 TCTT CTGACTTT TGT tll_chr3L_20630701_20630 + 2 1.02e-04 G CTGACTTC CCAGA tll_chr3R_12599144_12599 - 5 1.34e-04 TT TTGACCTT GGTG tll_chr3R_12527089_12527 - 5 1.64e-04 TTATCC TTGACTTA TGCA tll_chr3R_12526966_12526 - 11 2.25e-04 TGGTGATCA TTAACTTT TTGACGCCGC tll_chr3R_4526654_452668 - 23 3.30e-04 CGAG TTGCCTTC ATAAAATCTC tll_chr3R_12599286_12599 + 8 3.70e-04 TGACGAC CTGACCTT GGA tll_chr3L_20630476_20630 - 4 4.22e-04 TCTTT TTGGCTTT GAG tll_chr3L_20630429_20630 + 15 5.44e-04 ATGGCGGCAC TTAACTCT TTTT tll_chr3R_9720621_972063 + 6 5.95e-04 AACTT TTGCCTCT tll_chr2R_20730328_20730 + 6 8.02e-04 CTGCT TTAACTTA ATC tll_chr3R_4527125_452715 + 18 8.61e-04 GTCGGCGTCA TTGTCTTC TTT tll_chr3L_8639774_863978 - 2 1.06e-03 AGAA CTGACTCA G tll_chr3R_4527487_452750 + 8 1.19e-03 GCCATAT ATAACTTT AT tll_chr3R_12526878_12526 + 3 1.19e-03 TT ATGACCTC GTAAAAAAAC tll_chr3L_8640905_864092 - 4 1.74e-03 GAAAGAG TTGACACC GAA tll_chr2R_20730463_20730 + 2 2.92e-03 A TTAAATTT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- tll_chr3L_8641202_864123 3.1e-05 15_[-1]_6 tll_chr3L_20630381_20630 3.1e-05 4_[-1]_5 tll_chr3L_20630598_20630 3.1e-05 2_[+1]_7 tll_chr3L_20630716_20630 3.1e-05 10_[+1]_3 tll_chr2R_20730810_20730 5e-05 8_[-1]_3 tll_chr3R_9720721_972073 7e-05 4_[+1]_3 tll_chr3L_20630701_20630 0.0001 1_[+1]_5 tll_chr3R_12599144_12599 0.00013 4_[-1]_2 tll_chr3R_12527089_12527 0.00016 4_[-1]_6 tll_chr3R_12526966_12526 0.00022 10_[-1]_9 tll_chr3R_4526654_452668 0.00033 22_[-1]_4 tll_chr3R_12599286_12599 0.00037 7_[+1]_3 tll_chr3L_20630476_20630 0.00042 3_[-1]_5 tll_chr3L_20630429_20630 0.00054 14_[+1]_4 tll_chr3R_9720621_972063 0.0006 5_[+1] tll_chr2R_20730328_20730 0.0008 5_[+1]_3 tll_chr3R_4527125_452715 0.00086 17_[+1]_3 tll_chr3L_8639774_863978 0.0011 1_[-1]_4 tll_chr3R_4527487_452750 0.0012 7_[+1]_2 tll_chr3R_12526878_12526 0.0012 2_[+1]_15 tll_chr3L_8640905_864092 0.0017 3_[-1]_7 tll_chr2R_20730463_20730 0.0029 1_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=22 tll_chr3L_8641202_864123 ( 16) TTGACTTT 1 tll_chr3L_20630381_20630 ( 5) TTGACTTT 1 tll_chr3L_20630598_20630 ( 3) TTGACTTT 1 tll_chr3L_20630716_20630 ( 11) TTGACTTT 1 tll_chr2R_20730810_20730 ( 9) TTGACTTC 1 tll_chr3R_9720721_972073 ( 5) CTGACTTT 1 tll_chr3L_20630701_20630 ( 2) CTGACTTC 1 tll_chr3R_12599144_12599 ( 5) TTGACCTT 1 tll_chr3R_12527089_12527 ( 5) TTGACTTA 1 tll_chr3R_12526966_12526 ( 11) TTAACTTT 1 tll_chr3R_4526654_452668 ( 23) TTGCCTTC 1 tll_chr3R_12599286_12599 ( 8) CTGACCTT 1 tll_chr3L_20630476_20630 ( 4) TTGGCTTT 1 tll_chr3L_20630429_20630 ( 15) TTAACTCT 1 tll_chr3R_9720621_972063 ( 6) TTGCCTCT 1 tll_chr2R_20730328_20730 ( 6) TTAACTTA 1 tll_chr3R_4527125_452715 ( 18) TTGTCTTC 1 tll_chr3L_8639774_863978 ( 2) CTGACTCA 1 tll_chr3R_4527487_452750 ( 8) ATAACTTT 1 tll_chr3R_12526878_12526 ( 3) ATGACCTC 1 tll_chr3L_8640905_864092 ( 4) TTGACACC 1 tll_chr2R_20730463_20730 ( 2) TTAAATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 377 bayes= 5.60304 E= 4.1e-006 -174 -10 -1110 125 -1110 -1110 -1110 171 -42 -1110 198 -1110 142 -110 -210 -274 -274 229 -1110 -1110 -274 -52 -1110 142 -1110 -10 -1110 142 -116 48 -1110 96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.1e-006 0.090909 0.181818 0.000000 0.727273 0.000000 0.000000 0.000000 1.000000 0.227273 0.000000 0.772727 0.000000 0.818182 0.090909 0.045455 0.045455 0.045455 0.954545 0.000000 0.000000 0.045455 0.136364 0.000000 0.818182 0.000000 0.181818 0.000000 0.818182 0.136364 0.272727 0.000000 0.590909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TT[GA]ACTT[TC] -------------------------------------------------------------------------------- Time 0.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- tll_chr2R_20730463_20730 1.74e-02 10 tll_chr3L_20630716_20630 8.55e-04 10_[+1(3.05e-05)]_3 tll_chr2R_20730905_20730 4.85e-01 9 tll_chr3L_8639774_863978 1.27e-02 13 tll_chr3R_4527314_452732 1.30e-01 13 tll_chr3L_8639157_863916 6.66e-01 13 tll_chr3L_20630429_20630 2.05e-02 26 tll_chr3L_20630598_20630 6.10e-04 2_[+1(3.05e-05)]_7 tll_chr3R_4527236_452725 9.89e-01 20 tll_chr3R_12526878_12526 4.19e-02 25 tll_chr2R_20730564_20730 2.54e-01 12 tll_chr3L_20630517_20630 5.38e-01 17 tll_chr3L_8639260_863927 3.51e-01 15 tll_chr2R_20730328_20730 1.43e-02 16 tll_chr3R_9720721_972073 1.11e-03 4_[+1(6.96e-05)]_3 tll_chr3R_4527002_452702 6.04e-01 21 tll_chr3R_4527523_452754 2.68e-01 20 tll_chr3R_12599144_12599 1.87e-03 14 tll_chr3R_12526966_12526 8.94e-03 27 tll_chr3R_12527089_12527 3.61e-03 18 tll_chr3R_4527487_452750 2.35e-02 17 tll_chr3R_4526654_452668 1.77e-02 34 tll_chr3L_8640905_864092 3.75e-02 18 tll_chr3L_8639319_863933 6.05e-01 15 tll_chr3R_12599286_12599 8.12e-03 18 tll_chr3L_20630381_20630 6.10e-04 4_[-1(3.05e-05)]_5 tll_chr3R_4527306_452731 1.00e+00 6 tll_chr2R_20730532_20730 5.60e-01 10 tll_chr2R_20730810_20730 1.20e-03 8_[-1(5.01e-05)]_3 tll_chr3R_4527125_452715 3.55e-02 28 tll_chr3L_20630476_20630 7.57e-03 16 tll_chr3R_4526813_452683 2.65e-01 19 tll_chr3L_8639597_863960 7.58e-01 13 tll_chr3R_9720621_972063 7.12e-03 13 tll_chr3L_8641202_864123 1.34e-03 15_[-1(3.05e-05)]_6 tll_chr3L_20630701_20630 1.42e-03 14 tll_chr2R_20730481_20730 4.97e-01 8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************