******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) 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= /Users/amedina/work_area/Regulon_matrix_eval/data/Sites_FNA_NR/LexA.19.fna ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ LexA|65834-65853 1.0000 40 LexA|91004-91023 1.0000 40 LexA|606863-606882 1.0000 40 LexA|711238-711257 1.0000 40 LexA|738568-738587 1.0000 40 LexA|738659-738678 1.0000 40 LexA|812655-812674 1.0000 40 LexA|832259-832278 1.0000 40 LexA|932351-932370 1.0000 40 LexA|1020162-1020181 1.0000 40 LexA|1120730-1120749 1.0000 40 LexA|1229931-1229950 1.0000 40 LexA|1229951-1229970 1.0000 40 LexA|1808183-1808202 1.0000 40 LexA|1808201-1808220 1.0000 40 LexA|1821506-1821525 1.0000 40 LexA|1928789-1928808 1.0000 40 LexA|1944050-1944069 1.0000 40 LexA|1944102-1944121 1.0000 40 LexA|2079301-2079320 1.0000 40 LexA|2194468-2194487 1.0000 40 LexA|2749749-2749768 1.0000 40 LexA|2749771-2749790 1.0000 40 LexA|2821851-2821870 1.0000 40 LexA|3208751-3208770 1.0000 40 LexA|3646003-3646022 1.0000 40 LexA|3815720-3815739 1.0000 40 LexA|3851322-3851341 1.0000 40 LexA|3995930-3995949 1.0000 40 LexA|4255050-4255069 1.0000 40 LexA|4255091-4255110 1.0000 40 LexA|4255112-4255131 1.0000 40 LexA|4271978-4271997 1.0000 40 LexA|4577939-4577958 1.0000 40 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /Users/amedina/work_area/Regulon_matrix_eval/data/Sites_FNA_NR/LexA.19.fna -dna -mod oops -revcomp -text -nostatus -minw 20 -maxw 20 -bfile /Users/amedina/work_area/Regulon_matrix_eval/data/bg_freqs/2nt_upstream-noorf_Escherichia_coli_K12-ovlp-2str.meme_bg model: mod= oops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 20 maxw= 20 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 34 maxsites= 34 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1360 N= 34 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.313 C 0.187 G 0.187 T 0.313 Background letter frequencies (from /Users/amedina/work_area/Regulon_matrix_eval/data/bg_freqs/2nt_upstream-noorf_Escherichia_coli_K12-ovlp-2str.meme_bg): A 0.294 C 0.206 G 0.206 T 0.294 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 20 sites = 34 llr = 430 E-value = 2.0e-088 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 447::::8:8485645:a11 pos.-specific C 111a::111:1:2124a::3 probability G 1:1::a2:1121:11:::91 matrix T 451:a:7171413231:::5 bits 2.3 * 2.0 * * * 1.8 *** * * 1.6 *** *** Relative 1.4 *** *** Entropy 1.1 *** *** (18.3 bits) 0.9 *** ** * *** 0.7 ******** * *** 0.5 ******** * **** 0.2 ************** ***** 0.0 -------------------- Multilevel ATACTGTATAAAAAAACAGT consensus TA T TTTC C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------- LexA|2079301-2079320 + 10 2.30e-11 TTTGCAACT ATACTGTATATAAAAACAGT ATCAATGGAG LexA|2749749-2749768 + 10 3.92e-11 CCAGCCTCT TTACTGTATATAAAACCAGT TTATACTGTA LexA|3851322-3851341 - 12 2.28e-10 TATAGAAGT TTACTGTATAAATAAACAGT AATATTTGGA LexA|812655-812674 - 12 6.49e-10 CAACAAATT ATACTGGATAAAAAAACAGT TCATCACCAT LexA|1229951-1229970 + 10 7.96e-10 AAGAACAGA CTACTGTATATAAAAACAGT ATAACTTCAG LexA|1928789-1928808 + 10 1.48e-09 AAAAGAAAT ATACTGTATAAAATCACAGT TATTATGAGA LexA|3815720-3815739 + 10 3.25e-09 AGATACTCA CAACTGTATATAAATACAGT TACAGATTTA LexA|606863-606882 + 10 5.58e-09 AAACAGGAC TCACTGTATAAATAAACAGC TATTTTGTTG LexA|4255112-4255131 + 10 1.06e-08 CTCACAGCA TAACTGTATATACACCCAGG GGGCGGAATG LexA|1120730-1120749 + 10 2.20e-08 AGGTTATTT TACCTGTATAAATAACCAGT ATATTCAACA LexA|1821506-1821525 + 10 3.34e-08 CCGCCTGTT ACACTGGATAGATAACCAGC ATTCGGAGTC LexA|1944050-1944069 - 12 7.18e-08 GATAAAAAA ATGCTGGATAGATATCCAGC GAAGGATGAA LexA|3995930-3995949 + 10 8.11e-08 TAATCAGCA AATCTGTATATATACCCAGC TTTTTGGCGG LexA|2749771-2749790 + 10 8.11e-08 AACCAGTTT ATACTGTACACAATAACAGT AATGGTTTTT LexA|4255091-4255110 + 10 9.14e-08 AATCGCCTT TTGCTGTATATACTCACAGC ATAACTGTAT LexA|1020162-1020181 - 9 1.03e-07 CCCCTGTGAG TTACTGTATGGATGTACAGT ACATCCAG LexA|832259-832278 - 12 1.16e-07 AAACCTGAA ATACTGTATAAACAGCCAAT ATTGTGGCAT LexA|3646003-3646022 - 12 1.63e-07 CCTCAGAGC TAACTGGATAATCATACAGT ACATGCAGGT LexA|2821851-2821870 + 10 2.02e-07 AAACACTTG ATACTGTATGAGCATACAGT ATAATTGCTT LexA|2194468-2194487 + 11 2.02e-07 CATCTGCATT CAACTGGATAAAATTACAGG GATGCAGAAT LexA|65834-65853 + 10 2.51e-07 GGGCAGTAA TGACTGTATAAAACCACAGC CAATCAAACG LexA|1808201-1808220 + 10 5.09e-07 AAAAATCCT ATACTGTACGTATCGACAGT TTAGTGAGTT LexA|932351-932370 - 12 6.17e-07 CCAGTACTG TTGCTGTATGGATTAACAGG AGTGTAATCA LexA|4271978-4271997 - 12 6.78e-07 TGCATTCCA ATACTGTATATTCATTCAGG TCAATTTGTG LexA|4577939-4577958 - 12 1.17e-06 CGCGCTAAA TACCTGTATATATCATCAGT AAATATGGGG LexA|4255050-4255069 - 12 1.94e-06 TGGAACCAT AAACTGCACAATAAACCAGA GATTTATCGA LexA|711238-711257 + 10 3.13e-06 TGATTAACG CAACTGATTAAAAACCCAGC GTCCGCGTCG LexA|738568-738587 - 12 5.26e-06 CCACGGCGA TAACTGTCGATAAGCGCAGC CAGCTGCTGG LexA|1808183-1808202 + 10 7.99e-06 CACTTCCGT GCACTGTATAAAAATCCTAT ACTGTACGTA LexA|738659-738678 - 12 4.41e-05 TTCGAAATA ACGCTGCCCTGAAAGCCAGG CGTCAGGATA LexA|1944102-1944121 + 9 7.20e-05 AATAAATT ATACTGTGCCATTTTTCAGT TCATCGAGAC LexA|3208751-3208770 + 11 8.66e-05 ATTTTGAAAT AAGCTGGCGTTGATGCCAGC GGCAAACCGA LexA|1229931-1229950 + 10 2.89e-04 ATCAGTATT GATCTGCTGGCAAGAACAGA CTACTGTATA LexA|91004-91023 + 17 6.53e-04 TCAGTTCTGC GTATTGCAGAGAGGACGAAT GCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LexA|2079301-2079320 2.3e-11 9_[+1]_11 LexA|2749749-2749768 3.9e-11 9_[+1]_11 LexA|3851322-3851341 2.3e-10 11_[-1]_9 LexA|812655-812674 6.5e-10 11_[-1]_9 LexA|1229951-1229970 8e-10 9_[+1]_11 LexA|1928789-1928808 1.5e-09 9_[+1]_11 LexA|3815720-3815739 3.3e-09 9_[+1]_11 LexA|606863-606882 5.6e-09 9_[+1]_11 LexA|4255112-4255131 1.1e-08 9_[+1]_11 LexA|1120730-1120749 2.2e-08 9_[+1]_11 LexA|1821506-1821525 3.3e-08 9_[+1]_11 LexA|1944050-1944069 7.2e-08 11_[-1]_9 LexA|3995930-3995949 8.1e-08 9_[+1]_11 LexA|2749771-2749790 8.1e-08 9_[+1]_11 LexA|4255091-4255110 9.1e-08 9_[+1]_11 LexA|1020162-1020181 1e-07 8_[-1]_12 LexA|832259-832278 1.2e-07 11_[-1]_9 LexA|3646003-3646022 1.6e-07 11_[-1]_9 LexA|2821851-2821870 2e-07 9_[+1]_11 LexA|2194468-2194487 2e-07 10_[+1]_10 LexA|65834-65853 2.5e-07 9_[+1]_11 LexA|1808201-1808220 5.1e-07 9_[+1]_11 LexA|932351-932370 6.2e-07 11_[-1]_9 LexA|4271978-4271997 6.8e-07 11_[-1]_9 LexA|4577939-4577958 1.2e-06 11_[-1]_9 LexA|4255050-4255069 1.9e-06 11_[-1]_9 LexA|711238-711257 3.1e-06 9_[+1]_11 LexA|738568-738587 5.3e-06 11_[-1]_9 LexA|1808183-1808202 8e-06 9_[+1]_11 LexA|738659-738678 4.4e-05 11_[-1]_9 LexA|1944102-1944121 7.2e-05 8_[+1]_12 LexA|3208751-3208770 8.7e-05 10_[+1]_10 LexA|1229931-1229950 0.00029 9_[+1]_11 LexA|91004-91023 0.00065 16_[+1]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=34 LexA|2079301-2079320 ( 10) ATACTGTATATAAAAACAGT 1 LexA|2749749-2749768 ( 10) TTACTGTATATAAAACCAGT 1 LexA|3851322-3851341 ( 12) TTACTGTATAAATAAACAGT 1 LexA|812655-812674 ( 12) ATACTGGATAAAAAAACAGT 1 LexA|1229951-1229970 ( 10) CTACTGTATATAAAAACAGT 1 LexA|1928789-1928808 ( 10) ATACTGTATAAAATCACAGT 1 LexA|3815720-3815739 ( 10) CAACTGTATATAAATACAGT 1 LexA|606863-606882 ( 10) TCACTGTATAAATAAACAGC 1 LexA|4255112-4255131 ( 10) TAACTGTATATACACCCAGG 1 LexA|1120730-1120749 ( 10) TACCTGTATAAATAACCAGT 1 LexA|1821506-1821525 ( 10) ACACTGGATAGATAACCAGC 1 LexA|1944050-1944069 ( 12) ATGCTGGATAGATATCCAGC 1 LexA|3995930-3995949 ( 10) AATCTGTATATATACCCAGC 1 LexA|2749771-2749790 ( 10) ATACTGTACACAATAACAGT 1 LexA|4255091-4255110 ( 10) TTGCTGTATATACTCACAGC 1 LexA|1020162-1020181 ( 9) TTACTGTATGGATGTACAGT 1 LexA|832259-832278 ( 12) ATACTGTATAAACAGCCAAT 1 LexA|3646003-3646022 ( 12) TAACTGGATAATCATACAGT 1 LexA|2821851-2821870 ( 10) ATACTGTATGAGCATACAGT 1 LexA|2194468-2194487 ( 11) CAACTGGATAAAATTACAGG 1 LexA|65834-65853 ( 10) TGACTGTATAAAACCACAGC 1 LexA|1808201-1808220 ( 10) ATACTGTACGTATCGACAGT 1 LexA|932351-932370 ( 12) TTGCTGTATGGATTAACAGG 1 LexA|4271978-4271997 ( 12) ATACTGTATATTCATTCAGG 1 LexA|4577939-4577958 ( 12) TACCTGTATATATCATCAGT 1 LexA|4255050-4255069 ( 12) AAACTGCACAATAAACCAGA 1 LexA|711238-711257 ( 10) CAACTGATTAAAAACCCAGC 1 LexA|738568-738587 ( 12) TAACTGTCGATAAGCGCAGC 1 LexA|1808183-1808202 ( 10) GCACTGTATAAAAATCCTAT 1 LexA|738659-738678 ( 12) ACGCTGCCCTGAAAGCCAGG 1 LexA|1944102-1944121 ( 9) ATACTGTGCCATTTTTCAGT 1 LexA|3208751-3208770 ( 11) AAGCTGGCGTTGATGCCAGC 1 LexA|1229931-1229950 ( 10) GATCTGCTGGCAAGAACAGA 1 LexA|91004-91023 ( 17) GTATTGCAGAGAGGACGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 714 bayes= 4.32193 E= 2.0e-088 59 -81 -122 27 27 -81 -281 77 132 -181 -49 -232 -1173 223 -1173 -332 -1173 -1173 -1173 177 -1173 -1173 228 -1173 -332 -81 -23 120 149 -122 -281 -232 -1173 -49 -81 132 138 -281 -49 -232 49 -181 -23 27 149 -1173 -181 -132 68 -23 -281 14 100 -122 -81 -51 49 0 -81 -15 77 89 -281 -173 -1173 223 -281 -1173 172 -1173 -1173 -332 -173 -1173 214 -1173 -232 36 -49 85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 34 E= 2.0e-088 0.441176 0.117647 0.088235 0.352941 0.352941 0.117647 0.029412 0.500000 0.735294 0.058824 0.147059 0.058824 0.000000 0.970588 0.000000 0.029412 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.029412 0.117647 0.176471 0.676471 0.823529 0.088235 0.029412 0.058824 0.000000 0.147059 0.117647 0.735294 0.764706 0.029412 0.147059 0.058824 0.411765 0.058824 0.176471 0.352941 0.823529 0.000000 0.058824 0.117647 0.470588 0.176471 0.029412 0.323529 0.588235 0.088235 0.117647 0.205882 0.411765 0.205882 0.117647 0.264706 0.500000 0.382353 0.029412 0.088235 0.000000 0.970588 0.029412 0.000000 0.970588 0.000000 0.000000 0.029412 0.088235 0.000000 0.911765 0.000000 0.058824 0.264706 0.147059 0.529412 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][TA]ACTGTATA[AT]A[AT][AT][ATC][AC]CAG[TC] -------------------------------------------------------------------------------- Time 0.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LexA|65834-65853 1.05e-05 9_[+1(2.51e-07)]_11 LexA|91004-91023 2.71e-02 40 LexA|606863-606882 2.34e-07 9_[+1(5.58e-09)]_11 LexA|711238-711257 1.31e-04 9_[+1(3.13e-06)]_11 LexA|738568-738587 2.21e-04 11_[-1(5.26e-06)]_9 LexA|738659-738678 1.85e-03 11_[-1(4.41e-05)]_9 LexA|812655-812674 2.73e-08 11_[-1(6.49e-10)]_9 LexA|832259-832278 4.86e-06 11_[-1(1.16e-07)]_9 LexA|932351-932370 2.59e-05 11_[-1(6.17e-07)]_9 LexA|1020162-1020181 4.32e-06 8_[-1(1.03e-07)]_12 LexA|1120730-1120749 9.25e-07 9_[+1(2.20e-08)]_11 LexA|1229931-1229950 1.21e-02 40 LexA|1229951-1229970 3.34e-08 9_[+1(7.96e-10)]_11 LexA|1808183-1808202 3.36e-04 9_[+1(7.99e-06)]_11 LexA|1808201-1808220 2.14e-05 9_[+1(5.09e-07)]_11 LexA|1821506-1821525 1.40e-06 9_[+1(3.34e-08)]_11 LexA|1928789-1928808 6.23e-08 9_[+1(1.48e-09)]_11 LexA|1944050-1944069 3.01e-06 11_[-1(7.18e-08)]_9 LexA|1944102-1944121 3.02e-03 8_[+1(7.20e-05)]_12 LexA|2079301-2079320 9.67e-10 9_[+1(2.30e-11)]_11 LexA|2194468-2194487 8.50e-06 10_[+1(2.02e-07)]_10 LexA|2749749-2749768 1.65e-09 9_[+1(3.92e-11)]_11 LexA|2749771-2749790 3.41e-06 9_[+1(8.11e-08)]_11 LexA|2821851-2821870 8.50e-06 9_[+1(2.02e-07)]_11 LexA|3208751-3208770 3.63e-03 10_[+1(8.66e-05)]_10 LexA|3646003-3646022 6.83e-06 11_[-1(1.63e-07)]_9 LexA|3815720-3815739 1.37e-07 9_[+1(3.25e-09)]_11 LexA|3851322-3851341 9.57e-09 11_[-1(2.28e-10)]_9 LexA|3995930-3995949 3.41e-06 9_[+1(8.11e-08)]_11 LexA|4255050-4255069 8.15e-05 11_[-1(1.94e-06)]_9 LexA|4255091-4255110 3.84e-06 9_[+1(9.14e-08)]_11 LexA|4255112-4255131 4.44e-07 9_[+1(1.06e-08)]_11 LexA|4271978-4271997 2.85e-05 11_[-1(6.78e-07)]_9 LexA|4577939-4577958 4.90e-05 11_[-1(1.17e-06)]_9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: Magnolia.local ********************************************************************************