******************************************************************************** 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/Dref_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Dref_chr2L_10342665_1034 1.0000 8 Dref_chr3R_12030990_1203 1.0000 8 Dref_chrX_10590263_10590 1.0000 21 Dref_chrX_2196445_219645 1.0000 14 Dref_chr3R_17458945_1745 1.0000 8 Dref_chr3L_18787824_1878 1.0000 8 Dref_chr3R_8877769_88777 1.0000 8 Dref_chr2L_20756888_2075 1.0000 8 Dref_chr3R_12030978_1203 1.0000 8 Dref_chr3R_23064863_2306 1.0000 22 Dref_chr2L_20757380_2075 1.0000 8 Dref_chr3R_17497519_1749 1.0000 25 Dref_chr3R_17458956_1745 1.0000 16 Dref_chr3R_23064789_2306 1.0000 17 Dref_chr3R_23064812_2306 1.0000 22 Dref_chr3R_17497654_1749 1.0000 26 Dref_chr3R_8877723_88777 1.0000 8 Dref_chr3R_17497466_1749 1.0000 30 Dref_chr2L_20757791_2075 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/Dref_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= 19 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 273 N= 19 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.319 C 0.181 G 0.181 T 0.319 Background letter frequencies (from dataset with add-one prior applied): A 0.318 C 0.182 G 0.182 T 0.318 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 19 llr = 145 E-value = 3.9e-033 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 381:1a:9 pos.-specific C 2::9:::1 probability G ::119::: matrix T 628:::a1 bits 2.5 2.2 ** 2.0 ** 1.7 **** Information 1.5 **** content 1.2 ***** (11.0 bits) 1.0 ******* 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TATCGATA consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- Dref_chr3R_17497466_1749 + 10 3.42e-05 GCGGGAACA TATCGATA ACAGAGCTAC Dref_chr3R_17497654_1749 + 9 3.42e-05 TGGTAATA TATCGATA GGTGGCAGCG Dref_chr3R_17497519_1749 + 10 3.42e-05 GCAATGTAA TATCGATA GTGTCGTT Dref_chr3R_23064863_2306 + 7 3.42e-05 TATGCT TATCGATA AGAAAACT Dref_chr3R_8877769_88777 + 1 3.42e-05 . TATCGATA Dref_chr3L_18787824_1878 + 1 3.42e-05 . TATCGATA Dref_chrX_10590263_10590 + 8 3.42e-05 CGATATT TATCGATA GTCTCG Dref_chr2L_10342665_1034 + 1 3.42e-05 . TATCGATA Dref_chr3R_12030978_1203 + 1 5.38e-05 . CATCGATA Dref_chr3R_12030990_1203 + 1 5.38e-05 . CATCGATA Dref_chr2L_20757380_2075 + 1 8.79e-05 . AATCGATA Dref_chrX_2196445_219645 - 7 8.79e-05 . AATCGATA ACGATA Dref_chr2L_20756888_2075 - 1 1.22e-04 . TTTCGATA Dref_chr3R_17458956_1745 + 1 2.49e-04 . ATTCGATA TTACGATA Dref_chr2L_20757791_2075 + 1 3.37e-04 . TATGGATA Dref_chr3R_17458945_1745 + 1 3.94e-04 . AAACGATA Dref_chr3R_8877723_88777 + 1 5.66e-04 . AATCGATT Dref_chr3R_23064812_2306 - 12 9.43e-04 GAG CTGCGATA ACCGTGATCT Dref_chr3R_23064789_2306 + 8 3.01e-03 TGGGCGA TAACAATC AC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Dref_chr3R_17497466_1749 3.4e-05 9_[+1]_13 Dref_chr3R_17497654_1749 3.4e-05 8_[+1]_10 Dref_chr3R_17497519_1749 3.4e-05 9_[+1]_8 Dref_chr3R_23064863_2306 3.4e-05 6_[+1]_8 Dref_chr3R_8877769_88777 3.4e-05 [+1] Dref_chr3L_18787824_1878 3.4e-05 [+1] Dref_chrX_10590263_10590 3.4e-05 7_[+1]_6 Dref_chr2L_10342665_1034 3.4e-05 [+1] Dref_chr3R_12030978_1203 5.4e-05 [+1] Dref_chr3R_12030990_1203 5.4e-05 [+1] Dref_chr2L_20757380_2075 8.8e-05 [+1] Dref_chrX_2196445_219645 8.8e-05 6_[-1] Dref_chr2L_20756888_2075 0.00012 [-1] Dref_chr3R_17458956_1745 0.00025 [+1]_8 Dref_chr2L_20757791_2075 0.00034 [+1] Dref_chr3R_17458945_1745 0.00039 [+1] Dref_chr3R_8877723_88777 0.00057 [+1] Dref_chr3R_23064812_2306 0.00094 11_[-1]_3 Dref_chr3R_23064789_2306 0.003 7_[+1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=19 Dref_chr3R_17497466_1749 ( 10) TATCGATA 1 Dref_chr3R_17497654_1749 ( 9) TATCGATA 1 Dref_chr3R_17497519_1749 ( 10) TATCGATA 1 Dref_chr3R_23064863_2306 ( 7) TATCGATA 1 Dref_chr3R_8877769_88777 ( 1) TATCGATA 1 Dref_chr3L_18787824_1878 ( 1) TATCGATA 1 Dref_chrX_10590263_10590 ( 8) TATCGATA 1 Dref_chr2L_10342665_1034 ( 1) TATCGATA 1 Dref_chr3R_12030978_1203 ( 1) CATCGATA 1 Dref_chr3R_12030990_1203 ( 1) CATCGATA 1 Dref_chr2L_20757380_2075 ( 1) AATCGATA 1 Dref_chrX_2196445_219645 ( 7) AATCGATA 1 Dref_chr2L_20756888_2075 ( 1) TTTCGATA 1 Dref_chr3R_17458956_1745 ( 1) ATTCGATA 1 Dref_chr2L_20757791_2075 ( 1) TATGGATA 1 Dref_chr3R_17458945_1745 ( 1) AAACGATA 1 Dref_chr3R_8877723_88777 ( 1) AATCGATT 1 Dref_chr3R_23064812_2306 ( 12) CTGCGATA 1 Dref_chr3R_23064789_2306 ( 8) TAACAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 140 bayes= 4.63958 E= 3.9e-033 -27 -21 -1089 87 141 -1089 -1089 -101 -159 -1089 -179 141 -1089 238 -179 -1089 -259 -1089 238 -1089 165 -1089 -1089 -1089 -1089 -1089 -1089 165 149 -179 -1089 -259 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.9e-033 0.263158 0.157895 0.000000 0.578947 0.842105 0.000000 0.000000 0.157895 0.105263 0.000000 0.052632 0.842105 0.000000 0.947368 0.052632 0.000000 0.052632 0.000000 0.947368 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.894737 0.052632 0.000000 0.052632 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA]ATCGATA -------------------------------------------------------------------------------- Time 0.11 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Dref_chr2L_10342665_1034 6.83e-05 [+1(3.42e-05)] Dref_chr3R_12030990_1203 1.08e-04 [+1(5.38e-05)] Dref_chrX_10590263_10590 9.57e-04 7_[+1(3.42e-05)]_6 Dref_chrX_2196445_219645 1.23e-03 6_[-1(8.79e-05)] Dref_chr3R_17458945_1745 7.88e-04 8 Dref_chr3L_18787824_1878 6.83e-05 [+1(3.42e-05)] Dref_chr3R_8877769_88777 6.83e-05 [+1(3.42e-05)] Dref_chr2L_20756888_2075 2.44e-04 8 Dref_chr3R_12030978_1203 1.08e-04 [+1(5.38e-05)] Dref_chr3R_23064863_2306 1.02e-03 6_[+1(3.42e-05)]_8 Dref_chr2L_20757380_2075 1.76e-04 [+1(8.79e-05)] Dref_chr3R_17497519_1749 1.23e-03 9_[+1(3.42e-05)]_8 Dref_chr3R_17458956_1745 4.48e-03 16 Dref_chr3R_23064789_2306 5.85e-02 17 Dref_chr3R_23064812_2306 2.79e-02 22 Dref_chr3R_17497654_1749 1.30e-03 8_[+1(3.42e-05)]_10 Dref_chr3R_8877723_88777 1.13e-03 8 Dref_chr3R_17497466_1749 1.57e-03 9_[+1(3.42e-05)]_13 Dref_chr2L_20757791_2075 6.74e-04 8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************