******************************************************************************** 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/Dfd_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Dfd_chr2R_2013944_201395 1.0000 8 Dfd_chr3R_2613299_261330 1.0000 9 Dfd_chr3R_2613587_261359 1.0000 9 Dfd_chr3R_2612922_261292 1.0000 8 Dfd_chr3R_2613113_261312 1.0000 13 Dfd_chr3R_2613355_261336 1.0000 9 Dfd_chr3R_2612816_261282 1.0000 11 Dfd_chr2R_2013990_201400 1.0000 13 Dfd_chr2R_2014033_201404 1.0000 12 Dfd_chr3R_2613323_261334 1.0000 25 Dfd_chr3R_2613438_261344 1.0000 10 Dfd_chr3R_2612949_261296 1.0000 14 Dfd_chr2R_2013965_201397 1.0000 14 Dfd_chr3R_2613168_261317 1.0000 9 Dfd_chr3R_2613659_261366 1.0000 9 Dfd_chr3R_2613244_261325 1.0000 9 ******************************************************************************** ******************************************************************************** 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/Dfd_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= 16 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 182 N= 16 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.360 C 0.140 G 0.140 T 0.360 Background letter frequencies (from dataset with add-one prior applied): A 0.358 C 0.142 G 0.142 T 0.358 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 15 llr = 80 E-value = 3.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :199:15: pos.-specific C 1:11:::3 probability G 1::::331 matrix T 79::a615 bits 2.8 2.5 2.2 2.0 Information 1.7 content 1.4 * (7.7 bits) 1.1 **** 0.8 ***** * 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TTAATTAT consensus GGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- Dfd_chr3R_2613659_261366 + 1 1.44e-04 . TTAATGAC T Dfd_chr3R_2612949_261296 + 7 3.70e-04 GATGAC TTAATTAC Dfd_chr3R_2613587_261359 + 1 3.70e-04 . TTAATTGT T Dfd_chr3R_2613113_261312 - 4 4.94e-04 GC TTAATGAT GTT Dfd_chr3R_2613168_261317 - 2 5.27e-04 . CTAATTGC C Dfd_chr2R_2013990_201400 + 6 9.04e-04 CTACA TTAATTAT Dfd_chr3R_2613355_261336 + 1 1.14e-03 . GTAATGGG T Dfd_chr3R_2612816_261282 - 3 1.33e-03 T CTAATGAT AG Dfd_chr3R_2613438_261344 + 2 1.66e-03 T GTAATTAT T Dfd_chr3R_2613323_261334 - 1 1.86e-03 TCTGATTGAT TTAATTTC Dfd_chr2R_2013965_201397 - 6 2.28e-03 C TTAATAGC CGCCA Dfd_chr2R_2014033_201404 - 5 3.40e-03 . TTACTTAT CGCG Dfd_chr3R_2613299_261330 + 2 3.40e-03 C TTCATTAT Dfd_chr3R_2613244_261325 + 1 3.71e-03 . TAAATGGT C Dfd_chr2R_2013944_201395 + 1 3.71e-03 . TTAATTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Dfd_chr3R_2613659_261366 0.00014 [+1]_1 Dfd_chr3R_2612949_261296 0.00037 6_[+1] Dfd_chr3R_2613587_261359 0.00037 [+1]_1 Dfd_chr3R_2613113_261312 0.00049 3_[-1]_2 Dfd_chr3R_2613168_261317 0.00053 1_[-1] Dfd_chr2R_2013990_201400 0.0009 5_[+1] Dfd_chr3R_2613355_261336 0.0011 [+1]_1 Dfd_chr3R_2612816_261282 0.0013 2_[-1]_1 Dfd_chr3R_2613438_261344 0.0017 1_[+1]_1 Dfd_chr3R_2613323_261334 0.0019 [-1]_17 Dfd_chr2R_2013965_201397 0.0023 5_[-1]_1 Dfd_chr2R_2014033_201404 0.0034 4_[-1] Dfd_chr3R_2613299_261330 0.0034 1_[+1] Dfd_chr3R_2613244_261325 0.0037 [+1]_1 Dfd_chr2R_2013944_201395 0.0037 [+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=15 Dfd_chr3R_2613659_261366 ( 1) TTAATGAC 1 Dfd_chr3R_2612949_261296 ( 7) TTAATTAC 1 Dfd_chr3R_2613587_261359 ( 1) TTAATTGT 1 Dfd_chr3R_2613113_261312 ( 4) TTAATGAT 1 Dfd_chr3R_2613168_261317 ( 2) CTAATTGC 1 Dfd_chr2R_2013990_201400 ( 6) TTAATTAT 1 Dfd_chr3R_2613355_261336 ( 1) GTAATGGG 1 Dfd_chr3R_2612816_261282 ( 3) CTAATGAT 1 Dfd_chr3R_2613438_261344 ( 2) GTAATTAT 1 Dfd_chr3R_2613323_261334 ( 1) TTAATTTC 1 Dfd_chr2R_2013965_201397 ( 6) TTAATAGC 1 Dfd_chr2R_2014033_201404 ( 5) TTACTTAT 1 Dfd_chr3R_2613299_261330 ( 2) TTCATTAT 1 Dfd_chr3R_2613244_261325 ( 1) TAAATGGT 1 Dfd_chr2R_2013944_201395 ( 1) TTAATTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 70 bayes= 2.68859 E= 3.2e-008 -1055 -10 -10 104 -242 -1055 -1055 138 138 -109 -1055 -1055 138 -109 -1055 -1055 -1055 -1055 -1055 148 -242 -1055 123 75 58 -1055 123 -142 -1055 123 -10 58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 3.2e-008 0.000000 0.133333 0.133333 0.733333 0.066667 0.000000 0.000000 0.933333 0.933333 0.066667 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.066667 0.000000 0.333333 0.600000 0.533333 0.000000 0.333333 0.133333 0.000000 0.333333 0.133333 0.533333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTAAT[TG][AG][TC] -------------------------------------------------------------------------------- Time 0.05 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Dfd_chr2R_2013944_201395 7.41e-03 8 Dfd_chr3R_2613299_261330 1.35e-02 9 Dfd_chr3R_2613587_261359 1.48e-03 9 Dfd_chr3R_2612922_261292 2.23e-01 8 Dfd_chr3R_2613113_261312 5.91e-03 13 Dfd_chr3R_2613355_261336 4.57e-03 9 Dfd_chr3R_2612816_261282 1.06e-02 11 Dfd_chr2R_2013990_201400 1.08e-02 13 Dfd_chr2R_2014033_201404 3.35e-02 12 Dfd_chr3R_2613323_261334 6.50e-02 25 Dfd_chr3R_2613438_261344 9.90e-03 10 Dfd_chr3R_2612949_261296 5.17e-03 14 Dfd_chr2R_2013965_201397 3.14e-02 14 Dfd_chr3R_2613168_261317 2.11e-03 9 Dfd_chr3R_2613659_261366 5.76e-04 9 Dfd_chr3R_2613244_261325 1.48e-02 9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************