******************************************************************************** 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/slbo_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ slbo_chr3L_14044458_1404 1.0000 14 slbo_chrX_9898854_989886 1.0000 11 slbo_chrX_9898807_989882 1.0000 20 slbo_chr3L_14042362_1404 1.0000 12 slbo_chrX_9898779_989879 1.0000 19 slbo_chr3L_14042330_1404 1.0000 13 slbo_chr3L_14044316_1404 1.0000 19 slbo_chr3L_14044547_1404 1.0000 20 slbo_chr2R_19841710_1984 1.0000 22 slbo_chr3L_14042599_1404 1.0000 12 slbo_chr3L_14044414_1404 1.0000 34 slbo_chr3L_14044503_1404 1.0000 30 ******************************************************************************** ******************************************************************************** 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/slbo_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= 226 N= 12 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.319 C 0.181 G 0.181 T 0.319 Background letter frequencies (from dataset with add-one prior applied): A 0.317 C 0.183 G 0.183 T 0.317 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 12 llr = 68 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1231:118 pos.-specific C 3:::::8: probability G :44:6812 matrix T 643941:: bits 2.5 2.2 2.0 1.7 Information 1.5 ** content 1.2 ***** (8.2 bits) 1.0 ***** 0.7 * ***** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGGTGGCA consensus CTT T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- slbo_chr3L_14044414_1404 + 5 4.58e-05 GCCG TGTTGGCA ATAAAATATT slbo_chr2R_19841710_1984 - 7 1.49e-04 TATAAAAT CTGTTGCA TCACTG slbo_chr3L_14044547_1404 + 7 1.67e-04 AAAGAA TAGTGGCA CAATAG slbo_chrX_9898779_989879 - 8 2.86e-04 CCGC TGATTGCA ACATTGT slbo_chr3L_14042599_1404 + 2 3.61e-04 T TTTTTGCA ATC slbo_chr3L_14042330_1404 + 1 6.43e-04 . TGTTTGCG CACAT slbo_chr3L_14044503_1404 + 4 8.91e-04 GAG ATTTGGCA ATATTTATTG slbo_chr3L_14042362_1404 - 3 1.15e-03 GT TTGTGGAA GG slbo_chr3L_14044458_1404 - 4 1.15e-03 GAT CTGTGTCA TTT slbo_chr3L_14044316_1404 + 9 1.21e-03 GCTCATTA CGAAGGCA GGG slbo_chrX_9898807_989882 + 3 3.68e-03 AG TGATTACA AATTAAAATA slbo_chrX_9898854_989886 + 4 3.94e-03 CAT CAGTGGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- slbo_chr3L_14044414_1404 4.6e-05 4_[+1]_22 slbo_chr2R_19841710_1984 0.00015 6_[-1]_8 slbo_chr3L_14044547_1404 0.00017 6_[+1]_6 slbo_chrX_9898779_989879 0.00029 7_[-1]_4 slbo_chr3L_14042599_1404 0.00036 1_[+1]_3 slbo_chr3L_14042330_1404 0.00064 [+1]_5 slbo_chr3L_14044503_1404 0.00089 3_[+1]_19 slbo_chr3L_14042362_1404 0.0012 2_[-1]_2 slbo_chr3L_14044458_1404 0.0012 3_[-1]_3 slbo_chr3L_14044316_1404 0.0012 8_[+1]_3 slbo_chrX_9898807_989882 0.0037 2_[+1]_10 slbo_chrX_9898854_989886 0.0039 3_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=12 slbo_chr3L_14044414_1404 ( 5) TGTTGGCA 1 slbo_chr2R_19841710_1984 ( 7) CTGTTGCA 1 slbo_chr3L_14044547_1404 ( 7) TAGTGGCA 1 slbo_chrX_9898779_989879 ( 8) TGATTGCA 1 slbo_chr3L_14042599_1404 ( 2) TTTTTGCA 1 slbo_chr3L_14042330_1404 ( 1) TGTTTGCG 1 slbo_chr3L_14044503_1404 ( 4) ATTTGGCA 1 slbo_chr3L_14042362_1404 ( 3) TTGTGGAA 1 slbo_chr3L_14044458_1404 ( 4) CTGTGTCA 1 slbo_chr3L_14044316_1404 ( 9) CGAAGGCA 1 slbo_chrX_9898807_989882 ( 3) TGATTACA 1 slbo_chrX_9898854_989886 ( 4) CAGTGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 142 bayes= 3.43741 E= 1.4e-001 -193 87 -1023 88 -93 -1023 119 39 -34 -1023 119 7 -193 -1023 -1023 153 -1023 -1023 167 39 -193 -1023 219 -193 -193 219 -113 -1023 139 -1023 -13 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 1.4e-001 0.083333 0.333333 0.000000 0.583333 0.166667 0.000000 0.416667 0.416667 0.250000 0.000000 0.416667 0.333333 0.083333 0.000000 0.000000 0.916667 0.000000 0.000000 0.583333 0.416667 0.083333 0.000000 0.833333 0.083333 0.083333 0.833333 0.083333 0.000000 0.833333 0.000000 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC][GT][GTA]T[GT]GCA -------------------------------------------------------------------------------- Time 0.08 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- slbo_chr3L_14044458_1404 1.60e-02 14 slbo_chrX_9898854_989886 3.11e-02 11 slbo_chrX_9898807_989882 9.15e-02 20 slbo_chr3L_14042362_1404 1.15e-02 12 slbo_chrX_9898779_989879 6.85e-03 19 slbo_chr3L_14042330_1404 7.68e-03 13 slbo_chr3L_14044316_1404 2.87e-02 19 slbo_chr3L_14044547_1404 4.33e-03 20 slbo_chr2R_19841710_1984 4.46e-03 22 slbo_chr3L_14042599_1404 3.60e-03 12 slbo_chr3L_14044414_1404 2.47e-03 4_[+1(4.58e-05)]_22 slbo_chr3L_14044503_1404 4.02e-02 30 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************