******************************************************************************** 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/gcm_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ gcm_chr3R_14059348_14059 1.0000 14 gcm_chr3R_14060445_14060 1.0000 14 gcm_chr3R_14060045_14060 1.0000 14 gcm_chr3R_14060568_14060 1.0000 14 gcm_chr3R_14060762_14060 1.0000 14 gcm_chr3R_14059624_14059 1.0000 14 gcm_chr3R_14059835_14059 1.0000 14 gcm_chr3R_14058051_14058 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/gcm_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= 14 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= 112 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.250 C 0.250 G 0.250 T 0.250 Background letter frequencies (from dataset with add-one prior applied): A 0.250 C 0.250 G 0.250 T 0.250 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 7 sites = 8 llr = 64 E-value = 5.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::13:a: pos.-specific C aa9:a:: probability G :::6::1 matrix T :::1::9 bits 2.0 ** ** 1.8 ** ** 1.6 ** ** 1.4 *** *** Information 1.2 *** *** content 1.0 *** *** (11.6 bits) 0.8 ******* 0.6 ******* 0.4 ******* 0.2 ******* 0.0 ------- Multilevel CCCGCAT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- gcm_chr3R_14058051_14058 + 5 6.10e-05 AAAT CCCGCAT AAA gcm_chr3R_14059835_14059 + 5 6.10e-05 TTTG CCCGCAT TTC gcm_chr3R_14060045_14060 + 5 6.10e-05 CCGG CCCGCAT TGA gcm_chr3R_14059624_14059 + 5 1.22e-04 CAGA CCCACAT AAT gcm_chr3R_14060445_14060 + 5 1.22e-04 AATG CCCACAT GAT gcm_chr3R_14060762_14060 + 5 1.83e-04 ACCA CCCTCAT GAG gcm_chr3R_14060568_14060 + 5 3.05e-04 AGTA CCAGCAT CTG gcm_chr3R_14059348_14059 + 5 3.05e-04 CATA CCCGCAG TTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- gcm_chr3R_14058051_14058 6.1e-05 4_[+1]_3 gcm_chr3R_14059835_14059 6.1e-05 4_[+1]_3 gcm_chr3R_14060045_14060 6.1e-05 4_[+1]_3 gcm_chr3R_14059624_14059 0.00012 4_[+1]_3 gcm_chr3R_14060445_14060 0.00012 4_[+1]_3 gcm_chr3R_14060762_14060 0.00018 4_[+1]_3 gcm_chr3R_14060568_14060 0.00031 4_[+1]_3 gcm_chr3R_14059348_14059 0.00031 4_[+1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=7 seqs=8 gcm_chr3R_14058051_14058 ( 5) CCCGCAT 1 gcm_chr3R_14059835_14059 ( 5) CCCGCAT 1 gcm_chr3R_14060045_14060 ( 5) CCCGCAT 1 gcm_chr3R_14059624_14059 ( 5) CCCACAT 1 gcm_chr3R_14060445_14060 ( 5) CCCACAT 1 gcm_chr3R_14060762_14060 ( 5) CCCTCAT 1 gcm_chr3R_14060568_14060 ( 5) CCAGCAT 1 gcm_chr3R_14059348_14059 ( 5) CCCGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 64 bayes= 4.24793 E= 5.0e-007 -965 200 -965 -965 -965 200 -965 -965 -100 181 -965 -965 0 -965 132 -100 -965 200 -965 -965 200 -965 -965 -965 -965 -965 -100 181 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 8 E= 5.0e-007 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.250000 0.000000 0.625000 0.125000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CCC[GA]CAT -------------------------------------------------------------------------------- Time 0.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- gcm_chr3R_14059348_14059 4.87e-03 14 gcm_chr3R_14060445_14060 1.95e-03 14 gcm_chr3R_14060045_14060 9.77e-04 4_[+1(6.10e-05)]_3 gcm_chr3R_14060568_14060 4.87e-03 14 gcm_chr3R_14060762_14060 2.93e-03 14 gcm_chr3R_14059624_14059 1.95e-03 14 gcm_chr3R_14059835_14059 9.77e-04 4_[+1(6.10e-05)]_3 gcm_chr3R_14058051_14058 9.77e-04 4_[+1(6.10e-05)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************