******************************************************************************** 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/eve_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ eve_chr2R_5485759_548578 1.0000 24 eve_chr3R_12636941_12636 1.0000 12 eve_chr2R_5490987_549101 1.0000 25 eve_chr2R_15777994_15778 1.0000 23 eve_chr2R_20564746_20564 1.0000 26 eve_chr3R_17205862_17205 1.0000 36 eve_chr2R_7044643_704466 1.0000 22 eve_chr2R_15777955_15777 1.0000 17 eve_chr3R_12559847_12559 1.0000 86 eve_chr2R_5490935_549096 1.0000 33 eve_chr3R_12636897_12636 1.0000 15 eve_chr2R_20564632_20564 1.0000 19 eve_chr2R_7044683_704471 1.0000 36 eve_chr2R_20564544_20564 1.0000 10 eve_chr3R_12636987_12637 1.0000 16 eve_chr2R_7044520_704454 1.0000 26 eve_chr3R_12560060_12560 1.0000 47 eve_chr2R_15777851_15777 1.0000 45 eve_chr2R_5485790_548582 1.0000 37 eve_chr3R_12636916_12636 1.0000 14 ******************************************************************************** ******************************************************************************** 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/eve_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= 20 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 569 N= 20 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.334 C 0.166 G 0.166 T 0.334 Background letter frequencies (from dataset with add-one prior applied): A 0.333 C 0.167 G 0.167 T 0.333 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 15 sites = 9 llr = 101 E-value = 5.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :637128::94231: pos.-specific C 9:4233::11:6:78 probability G 1421:32:::4272: matrix T ::::61:a9:1:::2 bits 2.6 2.3 2.1 * 1.8 * Information 1.6 * * * content 1.3 * *** *** (16.2 bits) 1.0 ** **** **** 0.8 **** **** **** 0.5 ***** ********* 0.3 *************** 0.0 --------------- Multilevel CACATCATTAACGCC consensus GACCGG GAAGT sequence G A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- eve_chr2R_5490987_549101 + 8 1.13e-08 TCAGCAC CGCACGATTAGCACC GTT eve_chr2R_20564746_20564 + 3 4.72e-08 GT CGCATGATTAGGGGC CATTACAAA eve_chr2R_5490935_549096 + 4 2.56e-07 TCC CGCCTCGTTATCGCC GCTCAGCACC eve_chr2R_20564632_20564 + 1 5.15e-07 . CAAACCATTAACACC CGAA eve_chr3R_12560060_12560 - 20 2.53e-06 TTTTATTATC CACATTATCAGCGGC ATTATTGTTA eve_chr3R_12559847_12559 - 53 6.23e-06 AATAATCGTT CAAATCGTTAAAACC ATAAAAATAA eve_chr3R_17205862_17205 - 1 2.07e-05 CATGGCTCAT CAGGCAATTAAGGAC eve_chr2R_15777955_15777 - 1 2.16e-05 GA GGAATGATTAAAGCT eve_chr2R_5485790_548582 - 8 2.58e-05 CGACTCACCG CAGCAAATTCGCGCT GACTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- eve_chr2R_5490987_549101 1.1e-08 7_[+1]_3 eve_chr2R_20564746_20564 4.7e-08 2_[+1]_9 eve_chr2R_5490935_549096 2.6e-07 3_[+1]_15 eve_chr2R_20564632_20564 5.1e-07 [+1]_4 eve_chr3R_12560060_12560 2.5e-06 19_[-1]_13 eve_chr3R_12559847_12559 6.2e-06 52_[-1]_19 eve_chr3R_17205862_17205 2.1e-05 [-1]_21 eve_chr2R_15777955_15777 2.2e-05 [-1]_2 eve_chr2R_5485790_548582 2.6e-05 7_[-1]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=9 eve_chr2R_5490987_549101 ( 8) CGCACGATTAGCACC 1 eve_chr2R_20564746_20564 ( 3) CGCATGATTAGGGGC 1 eve_chr2R_5490935_549096 ( 4) CGCCTCGTTATCGCC 1 eve_chr2R_20564632_20564 ( 1) CAAACCATTAACACC 1 eve_chr3R_12560060_12560 ( 20) CACATTATCAGCGGC 1 eve_chr3R_12559847_12559 ( 53) CAAATCGTTAAAACC 1 eve_chr3R_17205862_17205 ( 1) CAGGCAATTAAGGAC 1 eve_chr2R_15777955_15777 ( 1) GGAATGATTAAAGCT 1 eve_chr2R_5485790_548582 ( 8) CAGCAAATTCGCGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 289 bayes= 4.23224 E= 5.5e-001 -982 241 -58 -982 74 -982 141 -982 0 141 41 -982 100 41 -58 -982 -158 100 -982 74 -58 100 100 -158 122 -982 41 -982 -982 -982 -982 158 -982 -58 -982 141 141 -58 -982 -982 41 -982 141 -158 -58 174 41 -982 0 -982 200 -982 -158 200 41 -982 -982 222 -982 -58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 5.5e-001 0.000000 0.888889 0.111111 0.000000 0.555556 0.000000 0.444444 0.000000 0.333333 0.444444 0.222222 0.000000 0.666667 0.222222 0.111111 0.000000 0.111111 0.333333 0.000000 0.555556 0.222222 0.333333 0.333333 0.111111 0.777778 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.888889 0.888889 0.111111 0.000000 0.000000 0.444444 0.000000 0.444444 0.111111 0.222222 0.555556 0.222222 0.000000 0.333333 0.000000 0.666667 0.000000 0.111111 0.666667 0.222222 0.000000 0.000000 0.777778 0.000000 0.222222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AG][CAG][AC][TC][CGA][AG]TTA[AG][CAG][GA][CG][CT] -------------------------------------------------------------------------------- Time 0.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- eve_chr2R_5485759_548578 1.54e-01 24 eve_chr3R_12636941_12636 1.00e+00 12 eve_chr2R_5490987_549101 2.48e-07 7_[+1(1.13e-08)]_3 eve_chr2R_15777994_15778 9.72e-01 23 eve_chr2R_20564746_20564 1.13e-06 2_[+1(4.72e-08)]_9 eve_chr3R_17205862_17205 9.10e-04 [-1(2.07e-05)]_21 eve_chr2R_7044643_704466 1.56e-01 22 eve_chr2R_15777955_15777 1.29e-04 [-1(2.16e-05)]_2 eve_chr3R_12559847_12559 8.97e-04 52_[-1(6.23e-06)]_19 eve_chr2R_5490935_549096 9.72e-06 3_[+1(2.56e-07)]_15 eve_chr3R_12636897_12636 4.44e-01 15 eve_chr2R_20564632_20564 5.15e-06 [+1(5.15e-07)]_4 eve_chr2R_7044683_704471 4.21e-01 36 eve_chr2R_20564544_20564 1.00e+00 10 eve_chr3R_12636987_12637 9.36e-02 16 eve_chr2R_7044520_704454 7.64e-01 26 eve_chr3R_12560060_12560 1.67e-04 19_[-1(2.53e-06)]_13 eve_chr2R_15777851_15777 9.55e-01 45 eve_chr2R_5485790_548582 1.19e-03 7_[-1(2.58e-05)]_15 eve_chr3R_12636916_12636 1.00e+00 14 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************