******************************************************************************** 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/twi_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ twi_chr3L_1445544_144555 1.0000 10 twi_chr3R_12599116_12599 1.0000 19 twi_chr3R_12526730_12526 1.0000 19 twi_chr2L_15474247_15474 1.0000 14 twi_chr3L_1445555_144556 1.0000 10 twi_chr3R_12526987_12527 1.0000 19 twi_chr3R_12527019_12527 1.0000 19 twi_chr3R_8895842_889584 1.0000 6 twi_chr3R_17203833_17203 1.0000 38 twi_chr3R_12526900_12526 1.0000 10 twi_chr3R_8895908_889591 1.0000 6 twi_chr3R_12599153_12599 1.0000 20 twi_chr2L_15474287_15474 1.0000 14 twi_chr3R_17205813_17205 1.0000 34 twi_chr3R_17205973_17205 1.0000 27 ******************************************************************************** ******************************************************************************** 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/twi_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= 15 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 265 N= 15 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.242 G 0.242 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.242 G 0.242 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 15 llr = 79 E-value = 1.0e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1a18:: pos.-specific C 9:522: probability G ::1:19 matrix T ::3:71 bits 2.0 * 1.8 * 1.6 ** * 1.4 ** * Information 1.2 ** * * content 1.0 ** * * (7.6 bits) 0.8 ** *** 0.6 ** *** 0.4 ****** 0.2 ****** 0.0 ------ Multilevel CACATG consensus TCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ twi_chr3R_17205813_17205 - 12 2.43e-04 ATGCGAATCA CACATG TTGACCAGCC twi_chr3R_12527019_12527 - 5 2.43e-04 GCTGAGCAA CACATG AGAA twi_chr3L_1445555_144556 + 3 2.43e-04 AG CACATG TT twi_chr3R_17205973_17205 + 6 5.03e-04 TGCAA CATATG GCGGCCATAT twi_chr3R_17203833_17203 + 5 5.03e-04 TGTA CATATG CACTACATAT twi_chr3R_8895842_889584 + 1 5.03e-04 . CATATG twi_chr3L_1445544_144555 + 3 5.03e-04 CG CATATG TT twi_chr2L_15474287_15474 - 7 7.31e-04 CG CACACG TGCGAG twi_chr3R_12526730_12526 - 8 7.31e-04 CCAGAA CACACG CTGTCCT twi_chr3R_8895908_889591 + 1 1.22e-03 . CACCTG twi_chr2L_15474247_15474 - 5 1.22e-03 CCAC CAAATG GCGA twi_chr3R_12526900_12526 + 3 3.64e-03 CA CACATT TC twi_chr3R_12526987_12527 + 5 5.56e-03 TCAC CATCGG CTCTGGAAC twi_chr3R_12599153_12599 + 6 8.99e-03 CAAAA CAGCCG TCGGCCATT twi_chr3R_12599116_12599 - 7 1.35e-02 AAGCGGA AAAAGG CAACAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- twi_chr3R_17205813_17205 0.00024 11_[-1]_17 twi_chr3R_12527019_12527 0.00024 4_[-1]_9 twi_chr3L_1445555_144556 0.00024 2_[+1]_2 twi_chr3R_17205973_17205 0.0005 5_[+1]_16 twi_chr3R_17203833_17203 0.0005 4_[+1]_28 twi_chr3R_8895842_889584 0.0005 [+1] twi_chr3L_1445544_144555 0.0005 2_[+1]_2 twi_chr2L_15474287_15474 0.00073 6_[-1]_2 twi_chr3R_12526730_12526 0.00073 7_[-1]_6 twi_chr3R_8895908_889591 0.0012 [+1] twi_chr2L_15474247_15474 0.0012 4_[-1]_4 twi_chr3R_12526900_12526 0.0036 2_[+1]_2 twi_chr3R_12526987_12527 0.0056 4_[+1]_9 twi_chr3R_12599153_12599 0.009 5_[+1]_9 twi_chr3R_12599116_12599 0.014 6_[-1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=15 twi_chr3R_17205813_17205 ( 12) CACATG 1 twi_chr3R_12527019_12527 ( 5) CACATG 1 twi_chr3L_1445555_144556 ( 3) CACATG 1 twi_chr3R_17205973_17205 ( 6) CATATG 1 twi_chr3R_17203833_17203 ( 5) CATATG 1 twi_chr3R_8895842_889584 ( 1) CATATG 1 twi_chr3L_1445544_144555 ( 3) CATATG 1 twi_chr2L_15474287_15474 ( 7) CACACG 1 twi_chr3R_12526730_12526 ( 8) CACACG 1 twi_chr3R_8895908_889591 ( 1) CACCTG 1 twi_chr2L_15474247_15474 ( 5) CAAATG 1 twi_chr3R_12526900_12526 ( 3) CACATT 1 twi_chr3R_12526987_12527 ( 5) CATCGG 1 twi_chr3R_12599153_12599 ( 6) CAGCCG 1 twi_chr3R_12599116_12599 ( 7) AAAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 190 bayes= 5.33286 E= 1.0e-006 -195 195 -1055 -1055 195 -1055 -1055 -1055 -95 95 -186 37 163 -27 -1055 -1055 -1055 -27 -86 137 -1055 -1055 195 -195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 15 E= 1.0e-006 0.066667 0.933333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.133333 0.466667 0.066667 0.333333 0.800000 0.200000 0.000000 0.000000 0.000000 0.200000 0.133333 0.666667 0.000000 0.000000 0.933333 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[CT][AC][TC]G -------------------------------------------------------------------------------- Time 0.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- twi_chr3L_1445544_144555 5.02e-03 10 twi_chr3R_12599116_12599 3.17e-01 19 twi_chr3R_12526730_12526 2.03e-02 19 twi_chr2L_15474247_15474 2.17e-02 14 twi_chr3L_1445555_144556 2.43e-03 10 twi_chr3R_12526987_12527 1.45e-01 19 twi_chr3R_12527019_12527 6.79e-03 19 twi_chr3R_8895842_889584 1.01e-03 6 twi_chr3R_17203833_17203 3.27e-02 38 twi_chr3R_12526900_12526 3.58e-02 10 twi_chr3R_8895908_889591 2.44e-03 6 twi_chr3R_12599153_12599 2.37e-01 20 twi_chr2L_15474287_15474 1.31e-02 14 twi_chr3R_17205813_17205 1.40e-02 34 twi_chr3R_17205973_17205 2.19e-02 27 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************