******************************************************************************** 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/Eip74EF_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Eip74EF_chr3L_15623028_1 1.0000 17 Eip74EF_chr3L_17553000_1 1.0000 21 Eip74EF_chr3L_15622831_1 1.0000 17 Eip74EF_chr3L_15622648_1 1.0000 17 Eip74EF_chr3L_17552907_1 1.0000 20 Eip74EF_chr3L_15622928_1 1.0000 18 Eip74EF_chr3L_17552797_1 1.0000 23 Eip74EF_chr3L_15622699_1 1.0000 15 ******************************************************************************** ******************************************************************************** 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/Eip74EF_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= 23 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= 148 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.311 C 0.189 G 0.189 T 0.311 Background letter frequencies (from dataset with add-one prior applied): A 0.309 C 0.191 G 0.191 T 0.309 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 8 llr = 60 E-value = 5.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 481:aa11 pos.-specific C 63:1:::1 probability G ::99::6: matrix T ::::::38 bits 2.4 2.2 1.9 * 1.7 **** Information 1.4 **** content 1.2 * **** (10.8 bits) 1.0 ****** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CAGGAAGT consensus AC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- Eip74EF_chr3L_17553000_1 - 7 1.96e-05 TGAATAA CCGGAAGT AACTCA Eip74EF_chr3L_15622699_1 + 3 3.92e-05 AC AAGGAAGT GTTAT Eip74EF_chr3L_15623028_1 + 10 4.67e-05 GTCCTAACT CAGGAAGC Eip74EF_chr3L_17552907_1 + 8 6.63e-05 GATTGAT CAGGAATT ATGGT Eip74EF_chr3L_15622831_1 - 2 2.61e-04 CATCGATC AAGGAAGA A Eip74EF_chr3L_15622928_1 - 5 3.20e-04 AAAATA CCAGAAGT TTTG Eip74EF_chr3L_15622648_1 - 3 3.52e-04 AAGCCAA AAGGAAAT CT Eip74EF_chr3L_17552797_1 - 1 4.18e-04 GTAGGAACAA CAGCAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Eip74EF_chr3L_17553000_1 2e-05 6_[-1]_7 Eip74EF_chr3L_15622699_1 3.9e-05 2_[+1]_5 Eip74EF_chr3L_15623028_1 4.7e-05 9_[+1] Eip74EF_chr3L_17552907_1 6.6e-05 7_[+1]_5 Eip74EF_chr3L_15622831_1 0.00026 1_[-1]_8 Eip74EF_chr3L_15622928_1 0.00032 4_[-1]_6 Eip74EF_chr3L_15622648_1 0.00035 2_[-1]_7 Eip74EF_chr3L_17552797_1 0.00042 [-1]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=8 Eip74EF_chr3L_17553000_1 ( 7) CCGGAAGT 1 Eip74EF_chr3L_15622699_1 ( 3) AAGGAAGT 1 Eip74EF_chr3L_15623028_1 ( 10) CAGGAAGC 1 Eip74EF_chr3L_17552907_1 ( 8) CAGGAATT 1 Eip74EF_chr3L_15622831_1 ( 2) AAGGAAGA 1 Eip74EF_chr3L_15622928_1 ( 5) CCAGAAGT 1 Eip74EF_chr3L_15622648_1 ( 3) AAGGAAAT 1 Eip74EF_chr3L_17552797_1 ( 1) CAGCAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 92 bayes= 3.39232 E= 5.1e-004 28 171 -965 -965 128 39 -965 -965 -130 -965 220 -965 -965 -61 220 -965 169 -965 -965 -965 169 -965 -965 -965 -130 -965 171 -31 -130 -61 -965 128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 5.1e-004 0.375000 0.625000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.125000 0.875000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.625000 0.250000 0.125000 0.125000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][AC]GGAA[GT]T -------------------------------------------------------------------------------- Time 0.05 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Eip74EF_chr3L_15623028_1 9.34e-04 9_[+1(4.67e-05)] Eip74EF_chr3L_17553000_1 5.48e-04 6_[-1(1.96e-05)]_7 Eip74EF_chr3L_15622831_1 5.21e-03 17 Eip74EF_chr3L_15622648_1 7.02e-03 17 Eip74EF_chr3L_17552907_1 1.72e-03 7_[+1(6.63e-05)]_5 Eip74EF_chr3L_15622928_1 7.02e-03 18 Eip74EF_chr3L_17552797_1 1.33e-02 23 Eip74EF_chr3L_15622699_1 6.27e-04 2_[+1(3.92e-05)]_5 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************