******************************************************************************** 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/z_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ z_chrX_2304147_2304152_D 1.0000 6 z_chr3R_12589741_1258975 1.0000 19 z_chrX_2651357_2651368_D 1.0000 12 z_chr3R_12589719_1258973 1.0000 19 z_chr3R_12481491_1248150 1.0000 10 z_chrX_2652777_2652782_D 1.0000 6 z_chr3R_12590108_1259012 1.0000 18 z_chr3R_12590730_1259075 1.0000 21 z_chr2L_2450912_2450917_ 1.0000 6 z_chr3L_17584665_1758468 1.0000 18 z_chrX_2653080_2653085_D 1.0000 6 z_chrX_2653883_2653888_D 1.0000 6 z_chr3R_12590579_1259059 1.0000 20 z_chr3R_12590301_1259033 1.0000 32 z_chr3R_12590699_1259072 1.0000 29 z_chrX_2653816_2653821_D 1.0000 6 z_chr3R_12560246_1256026 1.0000 15 z_chr3R_12589873_1258989 1.0000 18 z_chr3R_12560189_1256020 1.0000 16 z_chr3L_17584614_1758462 1.0000 16 z_chr3R_12590409_1259043 1.0000 30 z_chr2L_2450874_2450879_ 1.0000 6 z_chr3R_12590088_1259010 1.0000 16 z_chr3R_12590374_1259039 1.0000 25 z_chr3R_12560269_1256028 1.0000 15 z_chrX_2304183_2304188_D 1.0000 6 z_chrX_2651309_2651314_D 1.0000 6 z_chr2L_2450934_2450939_ 1.0000 6 z_chr3R_12589954_1258997 1.0000 21 z_chrX_2653989_2654004_D 1.0000 16 z_chr3R_12481458_1248146 1.0000 6 z_chrX_2652760_2652765_D 1.0000 6 z_chr3R_12589608_1258962 1.0000 17 z_chr3R_12560289_1256030 1.0000 16 z_chr3R_12589443_1258946 1.0000 25 z_chrX_2653050_2653055_D 1.0000 6 z_chr3R_12589999_1259001 1.0000 18 z_chr3R_12481511_1248151 1.0000 6 z_chrX_2653947_2653962_D 1.0000 16 z_chr3R_12560212_1256023 1.0000 19 z_chrX_2653846_2653851_D 1.0000 6 ******************************************************************************** ******************************************************************************** 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/z_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= 41 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 587 N= 41 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.278 C 0.222 G 0.222 T 0.278 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.223 G 0.223 T 0.277 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 41 llr = 235 E-value = 7.2e-048 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a:2: pos.-specific C 1:::21 probability G 1a:a:7 matrix T 7:::61 bits 2.2 * * 2.0 *** 1.7 *** 1.5 *** Information 1.3 *** content 1.1 *** (8.3 bits) 0.9 *** * 0.7 ****** 0.4 ****** 0.2 ****** 0.0 ------ Multilevel TGAGTG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ z_chrX_2653947_2653962_D - 6 2.35e-04 GCATT TGAGTG AGTTA z_chrX_2653050_2653055_D + 1 2.35e-04 . TGAGTG z_chr3R_12560289_1256030 + 8 2.35e-04 TCTCTCT TGAGTG TTC z_chrX_2652760_2652765_D + 1 2.35e-04 . TGAGTG z_chr2L_2450934_2450939_ - 1 2.35e-04 . TGAGTG z_chr3R_12590374_1259039 - 10 2.35e-04 AGTTTTTTTA TGAGTG CATCCAAAG z_chr2L_2450874_2450879_ - 1 2.35e-04 . TGAGTG z_chrX_2653816_2653821_D - 1 2.35e-04 . TGAGTG z_chrX_2653883_2653888_D + 1 2.35e-04 . TGAGTG z_chrX_2653080_2653085_D + 1 2.35e-04 . TGAGTG z_chr2L_2450912_2450917_ + 1 2.35e-04 . TGAGTG z_chr3R_12590108_1259012 + 4 2.35e-04 TTT TGAGTG CGTTCTTCC z_chrX_2652777_2652782_D + 1 2.35e-04 . TGAGTG z_chr3R_12481491_1248150 + 5 2.35e-04 CGAG TGAGTG z_chrX_2651357_2651368_D + 1 2.35e-04 . TGAGTG CACTCA z_chrX_2653846_2653851_D - 1 4.24e-04 . TGAGCG z_chrX_2304183_2304188_D + 1 4.24e-04 . TGAGCG z_chr3R_12560269_1256028 + 6 4.24e-04 GTTTT TGAGCG CTCT z_chr3L_17584614_1758462 - 6 4.24e-04 GTGCG TGAGCG GGTCT z_chr3R_12560246_1256026 - 8 4.24e-04 TT TGAGCG TTTCGCT z_chr3L_17584665_1758468 - 6 4.24e-04 GTGAACT TGAGCG TTTCT z_chr3R_12560212_1256023 + 9 8.48e-04 CCTAAAAA CGAGTG GAAAA z_chrX_2653989_2654004_D - 6 8.48e-04 ACAGG CGAGTG ACAAT z_chrX_2304147_2304152_D + 1 8.48e-04 . CGAGTG z_chrX_2651309_2651314_D - 1 1.08e-03 . TGAGTC z_chr3R_12560189_1256020 - 3 1.08e-03 GAGTGAGT TGAGTC GG z_chr3R_12590579_1259059 + 9 1.08e-03 TGTATCTA TGAGTC AGTTCT z_chr3R_12589999_1259001 + 5 1.38e-03 TTTT TGAGTT ATCGGCAC z_chr3R_12481458_1248146 + 1 1.91e-03 . GGAGTG z_chr3R_12590088_1259010 - 7 1.91e-03 AAAA TGAGCC ATAAAA z_chr3R_12590409_1259043 - 5 1.91e-03 GAGACTTTCA TGAGCC TTTA z_chr3R_12589608_1258962 + 2 2.33e-03 G CGAGAG CTTTTCATAG z_chr3R_12589741_1258975 + 7 2.95e-03 AACAAT TGAGAC AAACCAT z_chr3R_12481511_1248151 - 1 3.43e-03 . TGAGAT z_chr3R_12590730_1259075 + 6 3.43e-03 TCTTA TGAGAT AATTCACGAT z_chr3R_12589954_1258997 - 8 3.81e-03 CGTGCGTA AGAGCG AGATACA z_chr3R_12589873_1258989 + 5 3.81e-03 AGAG GGAGAG ATACGGTT z_chr3R_12590699_1259072 + 24 4.05e-03 AAGAAATTTT CGAGTT z_chr3R_12589719_1258973 + 12 4.92e-03 GCAAGGCGAA AGAGAG CA z_chr3R_12589443_1258946 - 14 6.39e-03 TGGAAA CGAGAT CGTTACGTTG z_chr3R_12590301_1259033 - 17 9.92e-03 TTCTGTTGCC GGAGCA ATTTGTCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- z_chrX_2653947_2653962_D 0.00024 5_[-1]_5 z_chrX_2653050_2653055_D 0.00024 [+1] z_chr3R_12560289_1256030 0.00024 7_[+1]_3 z_chrX_2652760_2652765_D 0.00024 [+1] z_chr2L_2450934_2450939_ 0.00024 [-1] z_chr3R_12590374_1259039 0.00024 9_[-1]_10 z_chr2L_2450874_2450879_ 0.00024 [-1] z_chrX_2653816_2653821_D 0.00024 [-1] z_chrX_2653883_2653888_D 0.00024 [+1] z_chrX_2653080_2653085_D 0.00024 [+1] z_chr2L_2450912_2450917_ 0.00024 [+1] z_chr3R_12590108_1259012 0.00024 3_[+1]_9 z_chrX_2652777_2652782_D 0.00024 [+1] z_chr3R_12481491_1248150 0.00024 4_[+1] z_chrX_2651357_2651368_D 0.00024 [+1]_6 z_chrX_2653846_2653851_D 0.00042 [-1] z_chrX_2304183_2304188_D 0.00042 [+1] z_chr3R_12560269_1256028 0.00042 5_[+1]_4 z_chr3L_17584614_1758462 0.00042 5_[-1]_5 z_chr3R_12560246_1256026 0.00042 7_[-1]_2 z_chr3L_17584665_1758468 0.00042 5_[-1]_7 z_chr3R_12560212_1256023 0.00085 8_[+1]_5 z_chrX_2653989_2654004_D 0.00085 5_[-1]_5 z_chrX_2304147_2304152_D 0.00085 [+1] z_chrX_2651309_2651314_D 0.0011 [-1] z_chr3R_12560189_1256020 0.0011 2_[-1]_8 z_chr3R_12590579_1259059 0.0011 8_[+1]_6 z_chr3R_12589999_1259001 0.0014 4_[+1]_8 z_chr3R_12481458_1248146 0.0019 [+1] z_chr3R_12590088_1259010 0.0019 6_[-1]_4 z_chr3R_12590409_1259043 0.0019 4_[-1]_20 z_chr3R_12589608_1258962 0.0023 1_[+1]_10 z_chr3R_12589741_1258975 0.003 6_[+1]_7 z_chr3R_12481511_1248151 0.0034 [-1] z_chr3R_12590730_1259075 0.0034 5_[+1]_10 z_chr3R_12589954_1258997 0.0038 7_[-1]_8 z_chr3R_12589873_1258989 0.0038 4_[+1]_8 z_chr3R_12590699_1259072 0.004 23_[+1] z_chr3R_12589719_1258973 0.0049 11_[+1]_2 z_chr3R_12589443_1258946 0.0064 13_[-1]_6 z_chr3R_12590301_1259033 0.0099 16_[-1]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=41 z_chrX_2653947_2653962_D ( 6) TGAGTG 1 z_chrX_2653050_2653055_D ( 1) TGAGTG 1 z_chr3R_12560289_1256030 ( 8) TGAGTG 1 z_chrX_2652760_2652765_D ( 1) TGAGTG 1 z_chr2L_2450934_2450939_ ( 1) TGAGTG 1 z_chr3R_12590374_1259039 ( 10) TGAGTG 1 z_chr2L_2450874_2450879_ ( 1) TGAGTG 1 z_chrX_2653816_2653821_D ( 1) TGAGTG 1 z_chrX_2653883_2653888_D ( 1) TGAGTG 1 z_chrX_2653080_2653085_D ( 1) TGAGTG 1 z_chr2L_2450912_2450917_ ( 1) TGAGTG 1 z_chr3R_12590108_1259012 ( 4) TGAGTG 1 z_chrX_2652777_2652782_D ( 1) TGAGTG 1 z_chr3R_12481491_1248150 ( 5) TGAGTG 1 z_chrX_2651357_2651368_D ( 1) TGAGTG 1 z_chrX_2653846_2653851_D ( 1) TGAGCG 1 z_chrX_2304183_2304188_D ( 1) TGAGCG 1 z_chr3R_12560269_1256028 ( 6) TGAGCG 1 z_chr3L_17584614_1758462 ( 6) TGAGCG 1 z_chr3R_12560246_1256026 ( 8) TGAGCG 1 z_chr3L_17584665_1758468 ( 6) TGAGCG 1 z_chr3R_12560212_1256023 ( 9) CGAGTG 1 z_chrX_2653989_2654004_D ( 6) CGAGTG 1 z_chrX_2304147_2304152_D ( 1) CGAGTG 1 z_chrX_2651309_2651314_D ( 1) TGAGTC 1 z_chr3R_12560189_1256020 ( 3) TGAGTC 1 z_chr3R_12590579_1259059 ( 9) TGAGTC 1 z_chr3R_12589999_1259001 ( 5) TGAGTT 1 z_chr3R_12481458_1248146 ( 1) GGAGTG 1 z_chr3R_12590088_1259010 ( 7) TGAGCC 1 z_chr3R_12590409_1259043 ( 5) TGAGCC 1 z_chr3R_12589608_1258962 ( 2) CGAGAG 1 z_chr3R_12589741_1258975 ( 7) TGAGAC 1 z_chr3R_12481511_1248151 ( 1) TGAGAT 1 z_chr3R_12590730_1259075 ( 6) TGAGAT 1 z_chr3R_12589954_1258997 ( 8) AGAGCG 1 z_chr3R_12589873_1258989 ( 5) GGAGAG 1 z_chr3R_12590699_1259072 ( 24) CGAGTT 1 z_chr3R_12589719_1258973 ( 12) AGAGAG 1 z_chr3R_12589443_1258946 ( 14) CGAGAT 1 z_chr3R_12590301_1259033 ( 17) GGAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 382 bayes= 5.24715 E= 7.2e-048 -251 -60 -160 140 -1200 -1200 217 -1200 185 -1200 -1200 -1200 -1200 -1200 217 -1200 -70 13 -1200 108 -350 -60 167 -119 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 41 E= 7.2e-048 0.048780 0.146341 0.073171 0.731707 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.170732 0.243902 0.000000 0.585366 0.024390 0.146341 0.707317 0.121951 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TGAG[TC]G -------------------------------------------------------------------------------- Time 0.26 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- z_chrX_2304147_2304152_D 1.70e-03 6 z_chr3R_12589741_1258975 7.95e-02 19 z_chrX_2651357_2651368_D 3.29e-03 12 z_chr3R_12589719_1258973 1.29e-01 19 z_chr3R_12481491_1248150 2.35e-03 10 z_chrX_2652777_2652782_D 4.71e-04 6 z_chr3R_12590108_1259012 6.10e-03 18 z_chr3R_12590730_1259075 1.04e-01 21 z_chr2L_2450912_2450917_ 4.71e-04 6 z_chr3L_17584665_1758468 1.10e-02 18 z_chrX_2653080_2653085_D 4.71e-04 6 z_chrX_2653883_2653888_D 4.71e-04 6 z_chr3R_12590579_1259059 3.20e-02 20 z_chr3R_12590301_1259033 4.16e-01 32 z_chr3R_12590699_1259072 1.77e-01 29 z_chrX_2653816_2653821_D 4.71e-04 6 z_chr3R_12560246_1256026 8.45e-03 15 z_chr3R_12589873_1258989 9.45e-02 18 z_chr3R_12560189_1256020 2.36e-02 16 z_chr3L_17584614_1758462 9.29e-03 16 z_chr3R_12590409_1259043 9.10e-02 30 z_chr2L_2450874_2450879_ 4.71e-04 6 z_chr3R_12590088_1259010 4.11e-02 16 z_chr3R_12590374_1259039 9.37e-03 25 z_chr3R_12560269_1256028 8.45e-03 15 z_chrX_2304183_2304188_D 8.48e-04 6 z_chrX_2651309_2651314_D 2.17e-03 6 z_chr2L_2450934_2450939_ 4.71e-04 6 z_chr3R_12589954_1258997 1.15e-01 21 z_chrX_2653989_2654004_D 1.85e-02 16 z_chr3R_12481458_1248146 3.81e-03 6 z_chrX_2652760_2652765_D 4.71e-04 6 z_chr3R_12589608_1258962 5.45e-02 17 z_chr3R_12560289_1256030 5.17e-03 16 z_chr3R_12589443_1258946 2.26e-01 25 z_chrX_2653050_2653055_D 4.71e-04 6 z_chr3R_12589999_1259001 3.52e-02 18 z_chr3R_12481511_1248151 6.86e-03 6 z_chrX_2653947_2653962_D 5.17e-03 16 z_chr3R_12560212_1256023 2.35e-02 19 z_chrX_2653846_2653851_D 8.48e-04 6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************