******************************************************************************** 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/ttk_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ttk_chr2R_5490909_549092 1.0000 21 ttk_chr2R_5490854_549088 1.0000 33 ttk_chr3R_2689863_268988 1.0000 19 ttk_chr2R_5485831_548584 1.0000 13 ttk_chr3R_2685247_268526 1.0000 19 ttk_chr3R_2689955_268997 1.0000 20 ttk_chr3R_26677882_26677 1.0000 9 ttk_chr3R_2689897_268991 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/ttk_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= 154 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.205 C 0.295 G 0.295 T 0.205 Background letter frequencies (from dataset with add-one prior applied): A 0.206 C 0.294 G 0.294 T 0.206 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 7 sites = 8 llr = 58 E-value = 4.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 49::a:4 pos.-specific C 6::::66 probability G :1aa::: matrix T :::::4: bits 2.3 * 2.1 * 1.8 *** 1.6 **** Information 1.4 **** content 1.1 **** (10.5 bits) 0.9 ******* 0.7 ******* 0.5 ******* 0.2 ******* 0.0 ------- Multilevel CAGGACC consensus A TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- ttk_chr2R_5485831_548584 + 3 9.34e-05 CG CAGGACC TTCT ttk_chr3R_2689863_268988 + 6 9.34e-05 GTTGC CAGGACC TCGGATA ttk_chr2R_5490854_549088 + 6 9.34e-05 ATGGC CAGGACC TCCTCATGGT ttk_chr2R_5490909_549092 - 7 9.34e-05 CGGAGGAG CAGGACC CGGAGC ttk_chr3R_26677882_26677 + 3 2.89e-04 CG CAGGATC ttk_chr3R_2689897_268991 + 7 4.26e-04 GCCTGC AAGGACA TTTCGCC ttk_chr3R_2685247_268526 - 9 4.58e-04 TAAT AAGGATA ACGTCCAT ttk_chr3R_2689955_268997 + 5 1.11e-03 GCGC AGGGATA TTTATGCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ttk_chr2R_5485831_548584 9.3e-05 2_[+1]_4 ttk_chr3R_2689863_268988 9.3e-05 5_[+1]_7 ttk_chr2R_5490854_549088 9.3e-05 5_[+1]_21 ttk_chr2R_5490909_549092 9.3e-05 6_[-1]_8 ttk_chr3R_26677882_26677 0.00029 2_[+1] ttk_chr3R_2689897_268991 0.00043 6_[+1]_7 ttk_chr3R_2685247_268526 0.00046 8_[-1]_4 ttk_chr3R_2689955_268997 0.0011 4_[+1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=7 seqs=8 ttk_chr2R_5485831_548584 ( 3) CAGGACC 1 ttk_chr3R_2689863_268988 ( 6) CAGGACC 1 ttk_chr2R_5490854_549088 ( 6) CAGGACC 1 ttk_chr2R_5490909_549092 ( 7) CAGGACC 1 ttk_chr3R_26677882_26677 ( 3) CAGGATC 1 ttk_chr3R_2689897_268991 ( 7) AAGGACA 1 ttk_chr3R_2685247_268526 ( 9) AAGGATA 1 ttk_chr3R_2689955_268997 ( 5) AGGGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 106 bayes= 3.61471 E= 4.1e-004 87 109 -965 -965 209 -965 -123 -965 -965 -965 176 -965 -965 -965 176 -965 228 -965 -965 -965 -965 109 -965 87 87 109 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 8 E= 4.1e-004 0.375000 0.625000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.625000 0.000000 0.375000 0.375000 0.625000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]AGGA[CT][CA] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- ttk_chr2R_5490909_549092 2.80e-03 6_[-1(9.34e-05)]_8 ttk_chr2R_5490854_549088 5.03e-03 5_[+1(9.34e-05)]_7_[-1(9.34e-05)]_7 ttk_chr3R_2689863_268988 2.43e-03 5_[+1(9.34e-05)]_7 ttk_chr2R_5485831_548584 1.31e-03 2_[+1(9.34e-05)]_4 ttk_chr3R_2685247_268526 1.18e-02 19 ttk_chr3R_2689955_268997 3.07e-02 20 ttk_chr3R_26677882_26677 1.73e-03 9 ttk_chr3R_2689897_268991 1.19e-02 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************