******************************************************************************** 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/Mad_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Mad_chr3R_2580148_258016 1.0000 20 Mad_chr3R_17209435_17209 1.0000 30 Mad_chr3R_21070780_21070 1.0000 30 Mad_chr3R_2580464_258049 1.0000 29 Mad_chr3R_17209509_17209 1.0000 22 Mad_chr2R_8412644_841266 1.0000 18 Mad_chr3R_2579983_257999 1.0000 13 Mad_chr3R_2580310_258032 1.0000 15 Mad_chr3R_17209380_17209 1.0000 29 Mad_chr2L_13905216_13905 1.0000 19 Mad_chr3R_17209467_17209 1.0000 17 Mad_chr3R_17209681_17209 1.0000 10 Mad_chr3R_2581266_258127 1.0000 13 Mad_chr3R_2580333_258034 1.0000 12 Mad_chr3R_2580045_258007 1.0000 28 Mad_chr3R_2580283_258029 1.0000 13 Mad_chr3R_17209607_17209 1.0000 18 Mad_chr3R_2579958_257997 1.0000 13 Mad_chr2R_8412650_841266 1.0000 12 Mad_chr3R_2580199_258021 1.0000 20 Mad_chr2R_8412627_841263 1.0000 8 Mad_chr3R_17209662_17209 1.0000 16 Mad_chr2L_13904760_13904 1.0000 14 ******************************************************************************** ******************************************************************************** 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/Mad_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= 23 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 419 N= 23 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.166 C 0.334 G 0.334 T 0.166 Background letter frequencies (from dataset with add-one prior applied): A 0.167 C 0.333 G 0.333 T 0.167 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 19 llr = 102 E-value = 2.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 216:12:7 pos.-specific C 6:3a:58: probability G 19::8323 matrix T 1:2:1::: bits 2.6 2.3 2.1 1.8 Information 1.6 * content 1.3 * * * (7.7 bits) 1.0 *** ** 0.8 **** ** 0.5 ***** ** 0.3 ******** 0.0 -------- Multilevel CGACGCCA consensus A C G G sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- Mad_chr3R_2579958_257997 + 5 8.57e-05 AGGT AGACGACA T Mad_chr2R_8412650_841266 + 1 1.24e-04 . CGACGGCA GCCA Mad_chr2R_8412644_841266 + 7 1.24e-04 GAATCG CGACGGCA GCCA Mad_chr3R_2580283_258029 - 3 3.91e-04 CAG CGCCGCCA CC Mad_chr3R_2581266_258127 - 3 3.91e-04 GGG CGCCGCCA GG Mad_chr3R_2580310_258032 - 3 4.10e-04 AGCCG CGACAACA GC Mad_chr3R_17209435_17209 - 20 5.05e-04 TGC CGCCGACA TTGAAAGACG Mad_chr3R_17209509_17209 - 5 5.62e-04 GCGCCGGTCT AGACTCCA GACC Mad_chr3R_21070780_21070 - 17 7.05e-04 AATGCC TGACGCCA CGCTGTCTGC Mad_chr2L_13905216_13905 + 5 1.05e-03 CATC AGACGCGA CTAAGCC Mad_chr3R_2580148_258016 - 2 1.10e-03 GTCTCTCACG CAACGCCA G Mad_chr3R_17209467_17209 - 5 1.44e-03 GCAAA CGTCGCCG CAAC Mad_chr3R_17209380_17209 + 16 1.96e-03 AGCCACGCCC CGTCGCGA AGGCGG Mad_chr3R_2579983_257999 + 2 2.17e-03 C CGCCGACG CATC Mad_chr3R_2580464_258049 + 1 2.48e-03 . CGACGCGG CGAATGCGAA Mad_chr3R_17209662_17209 - 3 3.46e-03 CAGCTG CGACAGCG GC Mad_chr2R_8412627_841263 - 1 4.80e-03 . GGCCGGCA Mad_chr3R_2580333_258034 - 3 4.80e-03 GC GGACGGCG AG Mad_chr3R_2580045_258007 - 21 5.79e-03 . AGTCTCCG AGGTGCCAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Mad_chr3R_2579958_257997 8.6e-05 4_[+1]_1 Mad_chr2R_8412650_841266 0.00012 [+1]_4 Mad_chr2R_8412644_841266 0.00012 6_[+1]_4 Mad_chr3R_2580283_258029 0.00039 2_[-1]_3 Mad_chr3R_2581266_258127 0.00039 2_[-1]_3 Mad_chr3R_2580310_258032 0.00041 2_[-1]_5 Mad_chr3R_17209435_17209 0.0005 19_[-1]_3 Mad_chr3R_17209509_17209 0.00056 4_[-1]_10 Mad_chr3R_21070780_21070 0.0007 16_[-1]_6 Mad_chr2L_13905216_13905 0.001 4_[+1]_7 Mad_chr3R_2580148_258016 0.0011 1_[-1]_11 Mad_chr3R_17209467_17209 0.0014 4_[-1]_5 Mad_chr3R_17209380_17209 0.002 15_[+1]_6 Mad_chr3R_2579983_257999 0.0022 1_[+1]_4 Mad_chr3R_2580464_258049 0.0025 [+1]_21 Mad_chr3R_17209662_17209 0.0035 2_[-1]_6 Mad_chr2R_8412627_841263 0.0048 [-1] Mad_chr3R_2580333_258034 0.0048 2_[-1]_2 Mad_chr3R_2580045_258007 0.0058 20_[-1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=19 Mad_chr3R_2579958_257997 ( 5) AGACGACA 1 Mad_chr2R_8412650_841266 ( 1) CGACGGCA 1 Mad_chr2R_8412644_841266 ( 7) CGACGGCA 1 Mad_chr3R_2580283_258029 ( 3) CGCCGCCA 1 Mad_chr3R_2581266_258127 ( 3) CGCCGCCA 1 Mad_chr3R_2580310_258032 ( 3) CGACAACA 1 Mad_chr3R_17209435_17209 ( 20) CGCCGACA 1 Mad_chr3R_17209509_17209 ( 5) AGACTCCA 1 Mad_chr3R_21070780_21070 ( 17) TGACGCCA 1 Mad_chr2L_13905216_13905 ( 5) AGACGCGA 1 Mad_chr3R_2580148_258016 ( 2) CAACGCCA 1 Mad_chr3R_17209467_17209 ( 5) CGTCGCCG 1 Mad_chr3R_17209380_17209 ( 16) CGTCGCGA 1 Mad_chr3R_2579983_257999 ( 2) CGCCGACG 1 Mad_chr3R_2580464_258049 ( 1) CGACGCGG 1 Mad_chr3R_17209662_17209 ( 3) CGACAGCG 1 Mad_chr2R_8412627_841263 ( 1) GGCCGGCA 1 Mad_chr3R_2580333_258034 ( 3) GGACGGCG 1 Mad_chr3R_2580045_258007 ( 21) AGTCTCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 258 bayes= 4.60254 E= 2.3e+000 34 92 -166 -166 -166 -1089 151 -1089 180 -34 -1089 -8 -1089 158 -1089 -1089 -66 -1089 124 -66 34 66 -34 -1089 -1089 134 -108 -1089 204 -1089 -8 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 2.3e+000 0.210526 0.631579 0.105263 0.052632 0.052632 0.000000 0.947368 0.000000 0.578947 0.263158 0.000000 0.157895 0.000000 1.000000 0.000000 0.000000 0.105263 0.000000 0.789474 0.105263 0.210526 0.526316 0.263158 0.000000 0.000000 0.842105 0.157895 0.000000 0.684211 0.000000 0.315789 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]G[AC]CG[CGA]C[AG] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- Mad_chr3R_2580148_258016 2.81e-02 20 Mad_chr3R_17209435_17209 2.30e-02 30 Mad_chr3R_21070780_21070 3.19e-02 30 Mad_chr3R_2580464_258049 1.04e-01 29 Mad_chr3R_17209509_17209 1.67e-02 22 Mad_chr2R_8412644_841266 2.72e-03 18 Mad_chr3R_2579983_257999 2.57e-02 13 Mad_chr3R_2580310_258032 6.53e-03 15 Mad_chr3R_17209380_17209 8.26e-02 29 Mad_chr2L_13905216_13905 2.48e-02 19 Mad_chr3R_17209467_17209 2.84e-02 17 Mad_chr3R_17209681_17209 8.92e-01 10 Mad_chr3R_2581266_258127 4.68e-03 13 Mad_chr3R_2580333_258034 4.69e-02 12 Mad_chr3R_2580045_258007 2.16e-01 28 Mad_chr3R_2580283_258029 4.68e-03 13 Mad_chr3R_17209607_17209 8.91e-01 18 Mad_chr3R_2579958_257997 1.03e-03 4_[+1(8.57e-05)]_1 Mad_chr2R_8412650_841266 1.24e-03 12 Mad_chr3R_2580199_258021 6.37e-01 20 Mad_chr2R_8412627_841263 9.57e-03 8 Mad_chr3R_17209662_17209 6.05e-02 16 Mad_chr2L_13904760_13904 6.69e-01 14 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************