******************************************************************************** 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/ovo_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ovo_chrX_8335007_8335031 1.0000 25 ovo_chrX_4909550_4909568 1.0000 19 ovo_chrX_4909155_4909183 1.0000 29 ovo_chrX_4909224_4909246 1.0000 23 ovo_chr3R_19106286_19106 1.0000 19 ovo_chrX_4909463_4909485 1.0000 23 ovo_chrX_6937188_6937207 1.0000 20 ovo_chrX_4908876_4908894 1.0000 19 ovo_chrX_4909379_4909403 1.0000 25 ovo_chrX_8334701_8334725 1.0000 25 ovo_chrX_6937587_6937607 1.0000 21 ovo_chrX_8334977_8335001 1.0000 25 ******************************************************************************** ******************************************************************************** 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/ovo_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= 273 N= 12 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.321 C 0.179 G 0.179 T 0.321 Background letter frequencies (from dataset with add-one prior applied): A 0.319 C 0.181 G 0.181 T 0.319 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 7 sites = 12 llr = 86 E-value = 5.6e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3:::92 pos.-specific C a5:1::6 probability G ::a::11 matrix T :3:9a:2 bits 2.5 * * 2.2 * * 2.0 * * 1.7 * * * Information 1.5 * * * content 1.2 * **** (10.3 bits) 1.0 * **** 0.7 * **** 0.5 ******* 0.2 ******* 0.0 ------- Multilevel CCGTTAC consensus A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- ovo_chrX_8334701_8334725 + 11 3.46e-05 GCACCTAGCA CCGTTAC ACGAAGAA ovo_chr3R_19106286_19106 + 7 3.46e-05 CAGGAA CCGTTAC TTCTGC ovo_chrX_4908876_4908894 - 12 1.57e-04 A CTGTTAC TGTAAGTTGT ovo_chrX_6937188_6937207 + 7 1.57e-04 GTTTTC CTGTTAC TTCTCTT ovo_chrX_4909463_4909485 + 9 1.57e-04 CCTTTTTA CAGTTAC ATAGCAAT ovo_chrX_4909224_4909246 - 10 1.57e-04 ATATTAA CAGTTAC ATTTAAAAT ovo_chrX_6937587_6937607 + 8 3.19e-04 AGAAGTT CCGTTAA TCGTACC ovo_chrX_4909155_4909183 + 12 3.19e-04 AAAAATAAAG CCGTTAA AATTGAATTT ovo_chrX_4909550_4909568 + 7 3.19e-04 GATTTT CCGTTGC TTTTTT ovo_chrX_8334977_8335001 + 11 9.26e-04 TAAAAAACTC CTGTTAT CGCCGTCT ovo_chrX_4909379_4909403 + 8 1.05e-03 ACGACTA CAGTTAG AATTAGAATG ovo_chrX_8335007_8335031 - 9 1.20e-03 ACAGATGATG CCGCTAT CGGTGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ovo_chrX_8334701_8334725 3.5e-05 10_[+1]_8 ovo_chr3R_19106286_19106 3.5e-05 6_[+1]_6 ovo_chrX_4908876_4908894 0.00016 11_[-1]_1 ovo_chrX_6937188_6937207 0.00016 6_[+1]_7 ovo_chrX_4909463_4909485 0.00016 8_[+1]_8 ovo_chrX_4909224_4909246 0.00016 9_[-1]_7 ovo_chrX_6937587_6937607 0.00032 7_[+1]_7 ovo_chrX_4909155_4909183 0.00032 11_[+1]_11 ovo_chrX_4909550_4909568 0.00032 6_[+1]_6 ovo_chrX_8334977_8335001 0.00093 10_[+1]_8 ovo_chrX_4909379_4909403 0.001 7_[+1]_11 ovo_chrX_8335007_8335031 0.0012 8_[-1]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=7 seqs=12 ovo_chrX_8334701_8334725 ( 11) CCGTTAC 1 ovo_chr3R_19106286_19106 ( 7) CCGTTAC 1 ovo_chrX_4908876_4908894 ( 12) CTGTTAC 1 ovo_chrX_6937188_6937207 ( 7) CTGTTAC 1 ovo_chrX_4909463_4909485 ( 9) CAGTTAC 1 ovo_chrX_4909224_4909246 ( 10) CAGTTAC 1 ovo_chrX_6937587_6937607 ( 8) CCGTTAA 1 ovo_chrX_4909155_4909183 ( 12) CCGTTAA 1 ovo_chrX_4909550_4909568 ( 7) CCGTTGC 1 ovo_chrX_8334977_8335001 ( 11) CTGTTAT 1 ovo_chrX_4909379_4909403 ( 8) CAGTTAG 1 ovo_chrX_8335007_8335031 ( 9) CCGCTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 201 bayes= 3.97728 E= 5.6e-008 -1023 247 -1023 -1023 -35 147 -1023 -35 -1023 -1023 247 -1023 -1023 -111 -1023 152 -1023 -1023 -1023 165 152 -1023 -111 -1023 -94 169 -111 -94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 12 E= 5.6e-008 0.000000 1.000000 0.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.083333 0.000000 0.916667 0.000000 0.000000 0.000000 1.000000 0.916667 0.000000 0.083333 0.000000 0.166667 0.583333 0.083333 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[CAT]GTTAC -------------------------------------------------------------------------------- Time 0.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ovo_chrX_8335007_8335031 4.45e-02 25 ovo_chrX_4909550_4909568 8.26e-03 19 ovo_chrX_4909155_4909183 1.46e-02 29 ovo_chrX_4909224_4909246 5.33e-03 23 ovo_chr3R_19106286_19106 9.00e-04 6_[+1(3.46e-05)]_6 ovo_chrX_4909463_4909485 5.33e-03 23 ovo_chrX_6937188_6937207 4.39e-03 20 ovo_chrX_4908876_4908894 4.08e-03 19 ovo_chrX_4909379_4909403 3.91e-02 25 ovo_chrX_8334701_8334725 1.31e-03 10_[+1(3.46e-05)]_8 ovo_chrX_6937587_6937607 9.52e-03 21 ovo_chrX_8334977_8335001 3.46e-02 25 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************