******************************************************************************** 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/Stat92E_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Stat92E_chr2R_5487511_54 1.0000 9 Stat92E_chr2R_5487632_54 1.0000 9 Stat92E_chrX_2196518_219 1.0000 9 ******************************************************************************** ******************************************************************************** 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/Stat92E_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= 9 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 3 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 27 N= 3 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.222 C 0.278 G 0.278 T 0.222 Background letter frequencies (from dataset with add-one prior applied): A 0.226 C 0.274 G 0.274 T 0.226 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 9 sites = 3 llr = 35 E-value = 2.0e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::::aa pos.-specific C ::a:7:::: probability G :::a3aa:: matrix T aa::::::: bits 2.1 ** ** 1.9 **** **** 1.7 **** **** 1.5 **** **** Information 1.3 **** **** content 1.1 **** **** (17.0 bits) 0.9 ********* 0.6 ********* 0.4 ********* 0.2 ********* 0.0 --------- Multilevel TTCGCGGAA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------- Stat92E_chrX_2196518_219 + 1 4.03e-06 . TTCGCGGAA Stat92E_chr2R_5487511_54 + 1 4.03e-06 . TTCGCGGAA Stat92E_chr2R_5487632_54 - 1 8.06e-06 . TTCGGGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Stat92E_chrX_2196518_219 4e-06 [+1] Stat92E_chr2R_5487511_54 4e-06 [+1] Stat92E_chr2R_5487632_54 8.1e-06 [-1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=9 seqs=3 Stat92E_chrX_2196518_219 ( 1) TTCGCGGAA 1 Stat92E_chr2R_5487511_54 ( 1) TTCGCGGAA 1 Stat92E_chr2R_5487632_54 ( 1) TTCGGGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 3 bayes= -1.45943 E= 2.0e-004 -823 -823 -823 214 -823 -823 -823 214 -823 186 -823 -823 -823 -823 186 -823 -823 128 28 -823 -823 -823 186 -823 -823 -823 186 -823 214 -823 -823 -823 214 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 3 E= 2.0e-004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTCG[CG]GGAA -------------------------------------------------------------------------------- Time 0.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Stat92E_chr2R_5487511_54 8.06e-06 [+1(4.03e-06)] Stat92E_chr2R_5487632_54 1.61e-05 [-1(8.06e-06)] Stat92E_chrX_2196518_219 8.06e-06 [+1(4.03e-06)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************