******************************************************************************** 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/br-Z4_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ br-Z4_chrX_3105849_31058 1.0000 17 br-Z4_chr2L_19115438_191 1.0000 13 br-Z4_chr2L_19115533_191 1.0000 14 br-Z4_chr2L_19115564_191 1.0000 16 br-Z4_chr2L_19115468_191 1.0000 11 br-Z4_chrX_3105915_31059 1.0000 40 br-Z4_chrX_3105784_31058 1.0000 32 br-Z4_chr2L_19115393_191 1.0000 17 ******************************************************************************** ******************************************************************************** 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/br-Z4_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= 160 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.369 C 0.131 G 0.131 T 0.369 Background letter frequencies (from dataset with add-one prior applied): A 0.366 C 0.134 G 0.134 T 0.366 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 4 llr = 27 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a::3:: pos.-specific C :38:8: probability G :8::38 matrix T ::38:3 bits 2.9 2.6 2.3 2.0 * * Information 1.7 ** ** content 1.4 *** ** (9.7 bits) 1.2 *** ** 0.9 *** ** 0.6 ****** 0.3 ****** 0.0 ------ Multilevel AGCTCG consensus CTAGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ br-Z4_chrX_3105849_31058 + 9 1.73e-04 TAAACTAA AGCTGG TGC br-Z4_chr2L_19115393_191 - 8 4.10e-04 TATT AGCTCT AACCATT br-Z4_chrX_3105915_31059 + 35 4.10e-04 GTGAAAGACA AGTTCG br-Z4_chrX_3105784_31058 + 26 5.40e-04 AATAAACAAA ACCACG A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- br-Z4_chrX_3105849_31058 0.00017 8_[+1]_3 br-Z4_chr2L_19115393_191 0.00041 7_[-1]_4 br-Z4_chrX_3105915_31059 0.00041 34_[+1] br-Z4_chrX_3105784_31058 0.00054 25_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=4 br-Z4_chrX_3105849_31058 ( 9) AGCTGG 1 br-Z4_chr2L_19115393_191 ( 8) AGCTCT 1 br-Z4_chrX_3105915_31059 ( 35) AGTTCG 1 br-Z4_chrX_3105784_31058 ( 26) ACCACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 120 bayes= 5.61471 E= 1.0e+003 145 -865 -865 -865 -865 90 248 -865 -865 248 -865 -55 -55 -865 -865 103 -865 248 90 -865 -865 -865 248 -55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 4 E= 1.0e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.000000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[GC][CT][TA][CG][GT] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- br-Z4_chrX_3105849_31058 4.15e-03 17 br-Z4_chr2L_19115438_191 5.14e-02 13 br-Z4_chr2L_19115533_191 5.55e-01 14 br-Z4_chr2L_19115564_191 4.78e-01 16 br-Z4_chr2L_19115468_191 3.47e-01 11 br-Z4_chrX_3105915_31059 2.83e-02 40 br-Z4_chrX_3105784_31058 2.87e-02 32 br-Z4_chr2L_19115393_191 9.79e-03 17 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************