******************************************************************************** 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/zen_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ zen_chr2R_7044520_704454 1.0000 26 zen_chr3R_17497594_17497 1.0000 33 zen_chr2R_7044683_704471 1.0000 36 zen_chr2L_13905145_13905 1.0000 17 zen_chr2R_15777955_15777 1.0000 17 zen_chr2R_15777851_15777 1.0000 45 zen_chr3R_12559847_12559 1.0000 86 zen_chr3R_12560060_12560 1.0000 47 zen_chr2L_13905029_13905 1.0000 20 zen_chr2L_13905234_13905 1.0000 26 zen_chr2R_7044643_704466 1.0000 22 zen_chr2R_15777994_15778 1.0000 20 ******************************************************************************** ******************************************************************************** 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/zen_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= 12 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 395 N= 12 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.386 C 0.114 G 0.114 T 0.386 Background letter frequencies (from dataset with add-one prior applied): A 0.385 C 0.115 G 0.115 T 0.385 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 12 llr = 66 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 8:2a82:4 pos.-specific C 1:2::334 probability G ::::3:71 matrix T 2a7::5:1 bits 3.1 2.8 2.5 2.2 * Information 1.9 * content 1.6 * (8.0 bits) 1.2 * * * 0.9 * ** * 0.6 ** ***** 0.3 ******** 0.0 -------- Multilevel ATTAATGA consensus GCCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- zen_chr2R_15777851_15777 + 38 1.68e-05 ATGACAATAC ATTAACGC zen_chr3R_12560060_12560 - 21 3.34e-04 TATCCACATT ATCAGCGG CATTATTGTT zen_chr3R_12559847_12559 + 75 4.22e-04 TTGAACGATT ATTAGCCA TAGT zen_chr2R_15777955_15777 - 2 4.22e-04 GAGGAATG ATTAAAGC T zen_chr2R_7044643_704466 + 5 5.20e-04 TTCA ATTAACCA GTTAAATGTG zen_chr2L_13905029_13905 + 4 7.07e-04 GAG ATAAGTGC CCATTAGTT zen_chr2L_13905145_13905 + 3 7.07e-04 AT ATTAATGA TCTTCCA zen_chr2L_13905234_13905 - 8 9.45e-04 ATTATTTATT TTTAATGC GAGATCG zen_chr3R_17497594_17497 + 2 1.07e-03 A CTTAATCC CAAATTGCAA zen_chr2R_7044683_704471 - 6 1.72e-03 TCAATTAAAT ATCAATCA ATTTC zen_chr2R_15777994_15778 - 13 6.19e-03 . ATTAAAGT AAATTTATTT zen_chr2R_7044520_704454 + 18 6.76e-03 TTGTTTTAAT TTAAATGA A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- zen_chr2R_15777851_15777 1.7e-05 37_[+1] zen_chr3R_12560060_12560 0.00033 20_[-1]_19 zen_chr3R_12559847_12559 0.00042 74_[+1]_4 zen_chr2R_15777955_15777 0.00042 1_[-1]_8 zen_chr2R_7044643_704466 0.00052 4_[+1]_10 zen_chr2L_13905029_13905 0.00071 3_[+1]_9 zen_chr2L_13905145_13905 0.00071 2_[+1]_7 zen_chr2L_13905234_13905 0.00095 7_[-1]_11 zen_chr3R_17497594_17497 0.0011 1_[+1]_24 zen_chr2R_7044683_704471 0.0017 5_[-1]_23 zen_chr2R_15777994_15778 0.0062 12_[-1] zen_chr2R_7044520_704454 0.0068 17_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=12 zen_chr2R_15777851_15777 ( 38) ATTAACGC 1 zen_chr3R_12560060_12560 ( 21) ATCAGCGG 1 zen_chr3R_12559847_12559 ( 75) ATTAGCCA 1 zen_chr2R_15777955_15777 ( 2) ATTAAAGC 1 zen_chr2R_7044643_704466 ( 5) ATTAACCA 1 zen_chr2L_13905029_13905 ( 4) ATAAGTGC 1 zen_chr2L_13905145_13905 ( 3) ATTAATGA 1 zen_chr2L_13905234_13905 ( 8) TTTAATGC 1 zen_chr3R_17497594_17497 ( 2) CTTAATCC 1 zen_chr2R_7044683_704471 ( 6) ATCAATCA 1 zen_chr2R_15777994_15778 ( 13) ATTAAAGT 1 zen_chr2R_7044520_704454 ( 18) TTAAATGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 311 bayes= 4.63904 E= 1.3e+003 96 -47 -1023 -121 -1023 -1023 -1023 138 -121 53 -1023 79 138 -1023 -1023 -1023 96 -1023 112 -1023 -121 153 -1023 38 -1023 153 253 -1023 12 185 -47 -220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 1.3e+003 0.750000 0.083333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.166667 0.166667 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.166667 0.333333 0.000000 0.500000 0.000000 0.333333 0.666667 0.000000 0.416667 0.416667 0.083333 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- ATTA[AG][TC][GC][AC] -------------------------------------------------------------------------------- Time 0.21 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- zen_chr2R_7044520_704454 2.27e-01 26 zen_chr3R_17497594_17497 5.39e-02 33 zen_chr2R_7044683_704471 9.49e-02 36 zen_chr2L_13905145_13905 1.40e-02 17 zen_chr2R_15777955_15777 8.41e-03 17 zen_chr2R_15777851_15777 1.27e-03 37_[+1(1.68e-05)] zen_chr3R_12559847_12559 6.46e-02 86 zen_chr3R_12560060_12560 2.64e-02 47 zen_chr2L_13905029_13905 1.82e-02 20 zen_chr2L_13905234_13905 3.53e-02 26 zen_chr2R_7044643_704466 1.55e-02 22 zen_chr2R_15777994_15778 1.49e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************