******************************************************************************** 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/Adf1_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Adf1_chr3R_2825152_28251 1.0000 23 Adf1_chr3R_2825118_28251 1.0000 27 Adf1_chr2L_19116304_1911 1.0000 18 Adf1_chr2L_2454658_24546 1.0000 28 Adf1_chr3R_2825019_28250 1.0000 41 Adf1_chr2L_14616172_1461 1.0000 38 Adf1_chr2L_14615473_1461 1.0000 37 ******************************************************************************** ******************************************************************************** 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/Adf1_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= 7 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 212 N= 7 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.156 C 0.344 G 0.344 T 0.156 Background letter frequencies (from dataset with add-one prior applied): A 0.157 C 0.343 G 0.343 T 0.157 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 11 sites = 7 llr = 67 E-value = 3.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::331::::14 pos.-specific C :a3:79:9::6 probability G 9::7::a::9: matrix T 1:4:11:1a:: bits 2.7 * 2.4 * 2.1 * 1.9 * Information 1.6 * * * content 1.3 * * * (13.8 bits) 1.1 ** * ****** 0.8 *********** 0.5 *********** 0.3 *********** 0.0 ----------- Multilevel GCTGCCGCTGC consensus AA A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------- Adf1_chr2L_19116304_1911 + 8 1.82e-06 GCAGTCC GCAGCCGCTGA Adf1_chr2L_2454658_24546 + 15 3.43e-06 CGGTCGCAGC GCTGCCGCTGC CGC Adf1_chr3R_2825019_28250 - 28 1.44e-05 GCT GCCACCGCTGA CTGCGCGCCG Adf1_chr2L_14615473_1461 + 1 1.97e-05 . GCTGCTGCTGC ATCCGTCGAC Adf1_chr3R_2825152_28251 - 6 2.66e-05 CGCGGTC GCAGTCGCTGC CAGTG Adf1_chr3R_2825118_28251 - 7 3.61e-05 CGCTGTTGCG GCCGACGCTGA CGCACA Adf1_chr2L_14616172_1461 - 8 1.01e-04 CTTTTCATTA TCTACCGTTAC GCGATCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Adf1_chr2L_19116304_1911 1.8e-06 7_[+1] Adf1_chr2L_2454658_24546 3.4e-06 14_[+1]_3 Adf1_chr3R_2825019_28250 1.4e-05 27_[-1]_3 Adf1_chr2L_14615473_1461 2e-05 [+1]_26 Adf1_chr3R_2825152_28251 2.7e-05 5_[-1]_7 Adf1_chr3R_2825118_28251 3.6e-05 6_[-1]_10 Adf1_chr2L_14616172_1461 0.0001 7_[-1]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=11 seqs=7 Adf1_chr2L_19116304_1911 ( 8) GCAGCCGCTGA 1 Adf1_chr2L_2454658_24546 ( 15) GCTGCCGCTGC 1 Adf1_chr3R_2825019_28250 ( 28) GCCACCGCTGA 1 Adf1_chr2L_14615473_1461 ( 1) GCTGCTGCTGC 1 Adf1_chr3R_2825152_28251 ( 6) GCAGTCGCTGC 1 Adf1_chr3R_2825118_28251 ( 7) GCCGACGCTGA 1 Adf1_chr2L_14616172_1461 ( 8) TCTACCGTTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 142 bayes= 4.26946 E= 3.1e-002 -945 -945 132 -14 -945 154 -945 -945 86 -26 -945 144 86 -945 106 -945 -14 106 -945 -14 -945 132 -945 -14 -945 -945 154 -945 -945 132 -945 -14 -945 -945 -945 267 -14 -945 132 -945 144 74 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 7 E= 3.1e-002 0.000000 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.285714 0.285714 0.000000 0.428571 0.285714 0.000000 0.714286 0.000000 0.142857 0.714286 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 1.000000 0.142857 0.000000 0.857143 0.000000 0.428571 0.571429 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GC[TAC][GA]CCGCTG[CA] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- Adf1_chr3R_2825152_28251 6.93e-04 5_[-1(2.66e-05)]_7 Adf1_chr3R_2825118_28251 1.23e-03 6_[-1(3.61e-05)]_10 Adf1_chr2L_19116304_1911 2.91e-05 7_[+1(1.82e-06)] Adf1_chr2L_2454658_24546 1.24e-04 14_[+1(3.43e-06)]_3 Adf1_chr3R_2825019_28250 8.90e-04 27_[-1(1.44e-05)]_3 Adf1_chr2L_14616172_1461 5.65e-03 38 Adf1_chr2L_14615473_1461 1.06e-03 [+1(1.97e-05)]_26 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************