******************************************************************************** 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/Top2_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Top2_chr3R_7783472_77835 1.0000 30 Top2_chr3R_7783072_77830 1.0000 21 Top2_chr3R_7783360_77833 1.0000 34 Top2_chr3R_7783127_77831 1.0000 51 ******************************************************************************** ******************************************************************************** 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/Top2_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= 4 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 136 N= 4 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.393 C 0.107 G 0.107 T 0.393 Background letter frequencies (from dataset with add-one prior applied): A 0.389 C 0.111 G 0.111 T 0.389 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 21 sites = 4 llr = 73 E-value = 6.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :53a:8:a38:a:83a:a:a: pos.-specific C ::3:3:::5:::a:::8:::: probability G :5::3::::3::::::3:::: matrix T a:5:53a:3:a::38:::a:a bits 3.2 * 2.9 * 2.5 * 2.2 * * Information 1.9 * * content 1.6 * * (26.3 bits) 1.3 ** * ** *** ****** 1.0 ** * ** **** ****** 0.6 ** ****************** 0.3 ********************* 0.0 --------------------- Multilevel TATATATACATACATACATAT consensus GA CT AG TA G sequence C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- Top2_chr3R_7783472_77835 + 7 2.12e-11 AACATA TGTACATACATACATACATAT GTA Top2_chr3R_7783127_77831 + 13 2.40e-10 TTGAACTACA TACATATACATACATACATAT GTATGTACTT Top2_chr3R_7783360_77833 + 7 1.21e-09 TGTATA TGTATATATGTACATACATAT GTACATA Top2_chr3R_7783072_77830 + 1 4.81e-08 . TAAAGTTAAATACTAAGATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Top2_chr3R_7783472_77835 2.1e-11 6_[+1]_3 Top2_chr3R_7783127_77831 2.4e-10 12_[+1]_18 Top2_chr3R_7783360_77833 1.2e-09 6_[+1]_7 Top2_chr3R_7783072_77830 4.8e-08 [+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 Top2_chr3R_7783472_77835 ( 7) TGTACATACATACATACATAT 1 Top2_chr3R_7783127_77831 ( 13) TACATATACATACATACATAT 1 Top2_chr3R_7783360_77833 ( 7) TGTATATATGTACATACATAT 1 Top2_chr3R_7783072_77830 ( 1) TAAAGTTAAATACTAAGATAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 56 bayes= 3.70044 E= 6.2e-003 -865 -865 -865 136 36 -865 217 -865 -64 117 -865 36 136 -865 -865 -865 -865 117 117 36 94 -865 -865 -64 -865 -865 -865 136 136 -865 -865 -865 -64 217 -865 -64 94 -865 117 -865 -865 -865 -865 136 136 -865 -865 -865 -865 317 -865 -865 94 -865 -865 -64 -64 -865 -865 94 136 -865 -865 -865 -865 276 117 -865 136 -865 -865 -865 -865 -865 -865 136 136 -865 -865 -865 -865 -865 -865 136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 6.2e-003 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 0.000000 0.250000 0.250000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.250000 0.000000 0.000000 0.750000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[AG][TAC]A[TCG][AT]TA[CAT][AG]TAC[AT][TA]A[CG]ATAT -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- Top2_chr3R_7783472_77835 4.24e-10 6_[+1(2.12e-11)]_3 Top2_chr3R_7783072_77830 9.62e-08 [+1(4.81e-08)] Top2_chr3R_7783360_77833 3.38e-08 6_[+1(1.21e-09)]_7 Top2_chr3R_7783127_77831 1.49e-08 12_[+1(2.40e-10)]_18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************