******************************************************************************** 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/sna_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ sna_chr3L_1445475_144548 1.0000 10 sna_chr3L_1445495_144550 1.0000 11 sna_chr3R_8895901_889592 1.0000 21 sna_chr3R_8898032_889807 1.0000 40 sna_chr3R_8896062_889607 1.0000 11 sna_chr3R_8898155_889817 1.0000 19 sna_chr3R_8896312_889633 1.0000 20 sna_chr3L_1445556_144556 1.0000 10 sna_chr3R_8898126_889814 1.0000 23 sna_chr3L_1445405_144541 1.0000 10 sna_chr3R_8897880_889791 1.0000 32 ******************************************************************************** ******************************************************************************** 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/sna_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= 11 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 207 N= 11 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.244 G 0.244 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.244 G 0.244 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 11 llr = 71 E-value = 2.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5911::1: pos.-specific C 5195:152 probability G :::::9:2 matrix T 1::5a:46 bits 2.0 * 1.8 * 1.6 ** ** 1.4 ** ** Information 1.2 ** ** content 1.0 ** ** (9.3 bits) 0.8 ** ** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AACCTGCT consensus C T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- sna_chr3R_8898155_889817 - 1 6.09e-05 ACCTTCTCAG CACTTGCT sna_chr3R_8897880_889791 + 13 1.25e-04 GGCAAAAGTC AACCTGTT GAATGCAGGA sna_chr3R_8898126_889814 - 8 1.25e-04 CCTGCAAT CACCTGTT TGCAACT sna_chr3L_1445405_144541 + 2 2.41e-04 C AACTTGCG G sna_chr3R_8898032_889807 - 4 2.41e-04 CTGAGAAAAC AACCTGCC ATT sna_chr3L_1445495_144550 - 3 2.41e-04 C CACTTGCG CT sna_chr3R_8895901_889592 + 8 4.89e-04 AGCTTCC CACCTGAT AGGACA sna_chr3L_1445556_144556 + 2 5.55e-04 G CACATGTT T sna_chr3R_8896312_889633 + 8 5.55e-04 CTCATCC TACCTGTT TCCAT sna_chr3L_1445475_144548 + 2 6.74e-04 C ACCTTGCT G sna_chr3R_8896062_889607 + 4 4.95e-03 TGG AAATTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sna_chr3R_8898155_889817 6.1e-05 [-1]_11 sna_chr3R_8897880_889791 0.00012 12_[+1]_12 sna_chr3R_8898126_889814 0.00012 7_[-1]_8 sna_chr3L_1445405_144541 0.00024 1_[+1]_1 sna_chr3R_8898032_889807 0.00024 3_[-1]_29 sna_chr3L_1445495_144550 0.00024 2_[-1]_1 sna_chr3R_8895901_889592 0.00049 7_[+1]_6 sna_chr3L_1445556_144556 0.00055 1_[+1]_1 sna_chr3R_8896312_889633 0.00055 7_[+1]_5 sna_chr3L_1445475_144548 0.00067 1_[+1]_1 sna_chr3R_8896062_889607 0.005 3_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=11 sna_chr3R_8898155_889817 ( 1) CACTTGCT 1 sna_chr3R_8897880_889791 ( 13) AACCTGTT 1 sna_chr3R_8898126_889814 ( 8) CACCTGTT 1 sna_chr3L_1445405_144541 ( 2) AACTTGCG 1 sna_chr3R_8898032_889807 ( 4) AACCTGCC 1 sna_chr3L_1445495_144550 ( 3) CACTTGCG 1 sna_chr3R_8895901_889592 ( 8) CACCTGAT 1 sna_chr3L_1445556_144556 ( 2) CACATGTT 1 sna_chr3R_8896312_889633 ( 8) TACCTGTT 1 sna_chr3L_1445475_144548 ( 2) ACCTTGCT 1 sna_chr3R_8896062_889607 ( 4) AAATTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 130 bayes= 3.43539 E= 2.6e-005 83 90 -1010 -149 183 -142 -1010 -1010 -149 190 -1010 -1010 -149 90 -1010 83 -1010 -1010 -1010 197 -1010 -142 190 -1010 -149 116 -1010 51 -1010 -42 -42 131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 2.6e-005 0.454545 0.454545 0.000000 0.090909 0.909091 0.090909 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.090909 0.454545 0.000000 0.454545 0.000000 0.000000 0.000000 1.000000 0.000000 0.090909 0.909091 0.000000 0.090909 0.545455 0.000000 0.363636 0.000000 0.181818 0.181818 0.636364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC]AC[CT]TG[CT]T -------------------------------------------------------------------------------- Time 0.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sna_chr3L_1445475_144548 4.03e-03 10 sna_chr3L_1445495_144550 1.93e-03 11 sna_chr3R_8895901_889592 1.36e-02 21 sna_chr3R_8898032_889807 1.58e-02 40 sna_chr3R_8896062_889607 3.89e-02 11 sna_chr3R_8898155_889817 1.46e-03 [-1(6.09e-05)]_11 sna_chr3R_8896312_889633 1.43e-02 20 sna_chr3L_1445556_144556 3.32e-03 10 sna_chr3R_8898126_889814 3.99e-03 23 sna_chr3L_1445405_144541 1.45e-03 10 sna_chr3R_8897880_889791 6.22e-03 32 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************