******************************************************************************** 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= ./meme.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1NC_000921.1 1.0000 35 2NC_000921.1 1.0000 35 3NC_000921.1 1.0000 35 4NC_000921.1 1.0000 35 5NC_000921.1 1.0000 35 6NC_000921.1 1.0000 35 7NC_000921.1 1.0000 35 8NC_000921.1 1.0000 35 9NC_000921.1 1.0000 35 10NC_000921.1 1.0000 35 11NC_000921.1 1.0000 35 12NC_000921.1 1.0000 35 13NC_000921.1 1.0000 35 14NC_000921.1 1.0000 35 15NC_000921.1 1.0000 35 16NC_000921.1 1.0000 35 17NC_000921.1 1.0000 35 18NC_000921.1 1.0000 35 19NC_000921.1 1.0000 35 20NC_000921.1 1.0000 35 21NC_000921.1 1.0000 35 22NC_000921.1 1.0000 35 23NC_000921.1 1.0000 35 24NC_000921.1 1.0000 35 25NC_000921.1 1.0000 35 26NC_000921.1 1.0000 35 27NC_000921.1 1.0000 35 28NC_000921.1 1.0000 35 29NC_000921.1 1.0000 35 30NC_000921.1 1.0000 35 31NC_000921.1 1.0000 35 32NC_000921.1 1.0000 35 33NC_000921.1 1.0000 35 34NC_000921.1 1.0000 35 35NC_000921.1 1.0000 35 36NC_000921.1 1.0000 35 37NC_000921.1 1.0000 35 38NC_000921.1 1.0000 35 39NC_000921.1 1.0000 35 40NC_000921.1 1.0000 35 41NC_000921.1 1.0000 35 42NC_000921.1 1.0000 35 43NC_000921.1 1.0000 35 44NC_000921.1 1.0000 35 45NC_000921.1 1.0000 35 46NC_000921.1 1.0000 35 47NC_000921.1 1.0000 35 48NC_000921.1 1.0000 35 49NC_000921.1 1.0000 35 50NC_000921.1 1.0000 35 51NC_000921.1 1.0000 35 52NC_000921.1 1.0000 35 53NC_000921.1 1.0000 35 54NC_000921.1 1.0000 35 55NC_000921.1 1.0000 35 56NC_000921.1 1.0000 35 57NC_000921.1 1.0000 35 58NC_000921.1 1.0000 35 59NC_000921.1 1.0000 35 60NC_000921.1 1.0000 35 61NC_000921.1 1.0000 35 62NC_000921.1 1.0000 35 63NC_000921.1 1.0000 35 64NC_000921.1 1.0000 35 65NC_000921.1 1.0000 35 66NC_000921.1 1.0000 35 67NC_000921.1 1.0000 35 68NC_000921.1 1.0000 35 69NC_000921.1 1.0000 35 70NC_000921.1 1.0000 35 71NC_000921.1 1.0000 35 72NC_000921.1 1.0000 35 73NC_000921.1 1.0000 35 74NC_000921.1 1.0000 35 75NC_000921.1 1.0000 35 76NC_000921.1 1.0000 35 77NC_000921.1 1.0000 35 78NC_000921.1 1.0000 35 79NC_000921.1 1.0000 35 80NC_000921.1 1.0000 35 81NC_000921.1 1.0000 35 82NC_000921.1 1.0000 35 83NC_000921.1 1.0000 35 84NC_000921.1 1.0000 35 85NC_000921.1 1.0000 35 86NC_000921.1 1.0000 35 87NC_000921.1 1.0000 35 88NC_000921.1 1.0000 35 89NC_000921.1 1.0000 35 90NC_000921.1 1.0000 35 91NC_000921.1 1.0000 35 92NC_000921.1 1.0000 35 93NC_000921.1 1.0000 35 94NC_000921.1 1.0000 35 95NC_000921.1 1.0000 35 96NC_000921.1 1.0000 35 97NC_000921.1 1.0000 35 98NC_000921.1 1.0000 35 99NC_000921.1 1.0000 35 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme ./meme.fasta -mod zoops -prior dirichlet -nostatus -dna -oc ./ model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 35 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 99 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= 3465 N= 99 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.366 C 0.135 G 0.172 T 0.327 Background letter frequencies (from dataset with add-one prior applied): A 0.366 C 0.135 G 0.172 T 0.327 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 11 sites = 27 llr = 206 E-value = 1.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 657::12::36 pos.-specific C 3::1122::1: probability G ::39973:::1 matrix T 14::::4aa64 bits 2.9 2.6 2.3 2.0 * Relative 1.7 ** * Entropy 1.4 *** ** (11.0 bits) 1.2 *** ** 0.9 **** ** 0.6 * **** *** 0.3 ****** **** 0.0 ----------- Multilevel AAAGGGTTTTA consensus CTG G AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- 79NC_000921.1 2 3.64e-06 A CTAGGGTTTTA TTTTTCATGT 78NC_000921.1 2 3.64e-06 A CTAGGGTTTTA TTTTTCATGT 43NC_000921.1 20 6.32e-06 GGTATCAACA ATAGGGGTTTA AAATT 8NC_000921.1 24 8.16e-06 TTATAACTAA AAGGGGGTTTT A 13NC_000921.1 24 2.07e-05 TTGTTTGGAT AAAGGGGTTCA A 70NC_000921.1 13 3.80e-05 AAAAATATTA AAAGGGTTTAA AAGTTTTTGT 6NC_000921.1 21 3.80e-05 TTACCGATAG CTAGGCTTTTA ATCT 55NC_000921.1 22 4.30e-05 ATCAAAAATA AAAGGGGTTAT TGA 67NC_000921.1 2 6.20e-05 T CTAGGCTTTTT GGGTTTAAAA 29NC_000921.1 1 6.76e-05 . CTAGGGATTAA AGGGTGTCCT 36NC_000921.1 18 8.20e-05 ACAAACAATT CAAGGGATTTG GCGATTT 33NC_000921.1 19 8.20e-05 ATTCCTGTAA ATGCGGTTTTA AATCTT 30NC_000921.1 19 8.20e-05 AATAATGAGT AAGGGGATTAA AATTCT 40NC_000921.1 9 8.98e-05 AGCAAGCC AAACGGCTTTT AATGAAAGGA 4NC_000921.1 2 1.18e-04 A AGGGGGCTTTT TCTAAAAAAA 71NC_000921.1 17 1.66e-04 CCCCACGAAA ACAGGGCTTAA GGATTTTC 68NC_000921.1 1 1.66e-04 . AAAGCGGTTCA TCATAATCGT 11NC_000921.1 19 1.66e-04 AAATTAGAGC ATGGGCGTTTG ATAGAA 50NC_000921.1 4 2.10e-04 AAC CAACGCTTTTT ACAAACAGCT 26NC_000921.1 17 2.10e-04 AAAAGAAAGA CAAGGATTTTA CAAGCAAG 53NC_000921.1 9 2.85e-04 TTTAAATC ATGGCGATTTT GTGTTGAAAG 42NC_000921.1 21 3.28e-04 TAATCTTGAA TTAGGGCTTAT TTTT 76NC_000921.1 18 3.50e-04 AAAAATTAGG CAGGAGTTTTA AAACTTT 44NC_000921.1 14 3.50e-04 AAATTTAGGG TAGCGGTTTTA GATTTTGACA 7NC_000921.1 14 4.24e-04 TGCTGGTTGA ATAGGGCGTAA TCTAGGCGCA 89NC_000921.1 24 5.48e-04 CATTTAATCA AAGGGAGTTCT A 5NC_000921.1 16 6.19e-04 AAGGTTTTTA AAAGCCATTTT AACACAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 79NC_000921.1 3.6e-06 1_[1]_23 78NC_000921.1 3.6e-06 1_[1]_23 43NC_000921.1 6.3e-06 19_[1]_5 8NC_000921.1 8.2e-06 23_[1]_1 13NC_000921.1 2.1e-05 23_[1]_1 70NC_000921.1 3.8e-05 12_[1]_12 6NC_000921.1 3.8e-05 20_[1]_4 55NC_000921.1 4.3e-05 21_[1]_3 67NC_000921.1 6.2e-05 1_[1]_23 29NC_000921.1 6.8e-05 [1]_24 36NC_000921.1 8.2e-05 17_[1]_7 33NC_000921.1 8.2e-05 18_[1]_6 30NC_000921.1 8.2e-05 18_[1]_6 40NC_000921.1 9e-05 8_[1]_16 4NC_000921.1 0.00012 1_[1]_23 71NC_000921.1 0.00017 16_[1]_8 68NC_000921.1 0.00017 [1]_24 11NC_000921.1 0.00017 18_[1]_6 50NC_000921.1 0.00021 3_[1]_21 26NC_000921.1 0.00021 16_[1]_8 53NC_000921.1 0.00028 8_[1]_16 42NC_000921.1 0.00033 20_[1]_4 76NC_000921.1 0.00035 17_[1]_7 44NC_000921.1 0.00035 13_[1]_11 7NC_000921.1 0.00042 13_[1]_11 89NC_000921.1 0.00055 23_[1]_1 5NC_000921.1 0.00062 15_[1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=11 seqs=27 79NC_000921.1 ( 2) CTAGGGTTTTA 1 78NC_000921.1 ( 2) CTAGGGTTTTA 1 43NC_000921.1 ( 20) ATAGGGGTTTA 1 8NC_000921.1 ( 24) AAGGGGGTTTT 1 13NC_000921.1 ( 24) AAAGGGGTTCA 1 70NC_000921.1 ( 13) AAAGGGTTTAA 1 6NC_000921.1 ( 21) CTAGGCTTTTA 1 55NC_000921.1 ( 22) AAAGGGGTTAT 1 67NC_000921.1 ( 2) CTAGGCTTTTT 1 29NC_000921.1 ( 1) CTAGGGATTAA 1 36NC_000921.1 ( 18) CAAGGGATTTG 1 33NC_000921.1 ( 19) ATGCGGTTTTA 1 30NC_000921.1 ( 19) AAGGGGATTAA 1 40NC_000921.1 ( 9) AAACGGCTTTT 1 4NC_000921.1 ( 2) AGGGGGCTTTT 1 71NC_000921.1 ( 17) ACAGGGCTTAA 1 68NC_000921.1 ( 1) AAAGCGGTTCA 1 11NC_000921.1 ( 19) ATGGGCGTTTG 1 50NC_000921.1 ( 4) CAACGCTTTTT 1 26NC_000921.1 ( 17) CAAGGATTTTA 1 53NC_000921.1 ( 9) ATGGCGATTTT 1 42NC_000921.1 ( 21) TTAGGGCTTAT 1 76NC_000921.1 ( 18) CAGGAGTTTTA 1 44NC_000921.1 ( 14) TAGCGGTTTTA 1 7NC_000921.1 ( 14) ATAGGGCGTAA 1 89NC_000921.1 ( 24) AAGGGAGTTCT 1 5NC_000921.1 ( 16) AAAGCCATTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2475 bayes= 7.7056 E= 1.5e-006 70 130 -1140 -214 50 -187 -221 32 87 -1140 96 -1140 -1140 13 231 -1140 -330 -28 231 -1140 -230 45 211 -1140 -98 45 59 18 -1140 -1140 -221 156 -1140 -1140 -1140 161 -50 -28 -1140 94 60 -1140 -121 18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 27 E= 1.5e-006 0.592593 0.333333 0.000000 0.074074 0.518519 0.037037 0.037037 0.407407 0.666667 0.000000 0.333333 0.000000 0.000000 0.148148 0.851852 0.000000 0.037037 0.111111 0.851852 0.000000 0.074074 0.185185 0.740741 0.000000 0.185185 0.185185 0.259259 0.370370 0.000000 0.000000 0.037037 0.962963 0.000000 0.000000 0.000000 1.000000 0.259259 0.111111 0.000000 0.629630 0.555556 0.000000 0.074074 0.370370 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AT][AG]GGG[TG]TT[TA][AT] -------------------------------------------------------------------------------- Time 2.57 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1NC_000921.1 9.82e-01 35 2NC_000921.1 9.86e-01 35 3NC_000921.1 3.40e-01 35 4NC_000921.1 2.95e-03 35 5NC_000921.1 1.54e-02 35 6NC_000921.1 9.51e-04 20_[1(3.80e-05)]_4 7NC_000921.1 1.05e-02 35 8NC_000921.1 2.04e-04 23_[1(8.16e-06)]_1 9NC_000921.1 4.22e-01 35 10NC_000921.1 2.95e-01 35 11NC_000921.1 4.14e-03 35 12NC_000921.1 1.83e-01 35 13NC_000921.1 5.19e-04 23_[1(2.07e-05)]_1 14NC_000921.1 9.67e-01 35 15NC_000921.1 3.89e-01 35 16NC_000921.1 6.81e-01 35 17NC_000921.1 5.55e-01 35 18NC_000921.1 8.18e-01 35 19NC_000921.1 5.02e-02 35 20NC_000921.1 4.56e-01 35 21NC_000921.1 4.65e-01 35 22NC_000921.1 9.34e-01 35 23NC_000921.1 8.65e-01 35 24NC_000921.1 8.03e-01 35 25NC_000921.1 9.16e-01 35 26NC_000921.1 5.24e-03 35 27NC_000921.1 2.20e-01 35 28NC_000921.1 8.55e-01 35 29NC_000921.1 1.69e-03 [1(6.76e-05)]_24 30NC_000921.1 2.05e-03 18_[1(8.20e-05)]_6 31NC_000921.1 8.23e-01 35 32NC_000921.1 7.33e-01 35 33NC_000921.1 2.05e-03 18_[1(8.20e-05)]_6 34NC_000921.1 7.33e-01 35 35NC_000921.1 2.01e-01 35 36NC_000921.1 2.05e-03 17_[1(8.20e-05)]_7 37NC_000921.1 4.31e-01 35 38NC_000921.1 4.31e-01 35 39NC_000921.1 2.95e-01 35 40NC_000921.1 2.24e-03 8_[1(8.98e-05)]_16 41NC_000921.1 7.53e-02 35 42NC_000921.1 8.17e-03 35 43NC_000921.1 1.58e-04 19_[1(6.32e-06)]_5 44NC_000921.1 8.70e-03 35 45NC_000921.1 7.05e-01 35 46NC_000921.1 6.50e-01 35 47NC_000921.1 8.46e-01 35 48NC_000921.1 1.92e-01 35 49NC_000921.1 9.20e-01 35 50NC_000921.1 5.24e-03 35 51NC_000921.1 8.08e-01 35 52NC_000921.1 1.22e-01 35 53NC_000921.1 7.10e-03 35 54NC_000921.1 8.79e-01 35 55NC_000921.1 1.07e-03 21_[1(4.30e-05)]_3 56NC_000921.1 1.96e-01 35 57NC_000921.1 2.61e-01 35 58NC_000921.1 1.71e-01 35 59NC_000921.1 9.24e-01 35 60NC_000921.1 2.26e-01 35 61NC_000921.1 4.22e-01 35 62NC_000921.1 9.58e-01 35 63NC_000921.1 4.68e-02 35 64NC_000921.1 3.03e-01 35 65NC_000921.1 2.31e-01 35 66NC_000921.1 1.22e-01 35 67NC_000921.1 1.55e-03 1_[1(6.20e-05)]_23 68NC_000921.1 4.14e-03 35 69NC_000921.1 3.56e-01 35 70NC_000921.1 9.51e-04 12_[1(3.80e-05)]_12 71NC_000921.1 4.14e-03 35 72NC_000921.1 5.23e-01 35 73NC_000921.1 1.83e-01 35 74NC_000921.1 9.69e-01 35 75NC_000921.1 6.93e-01 35 76NC_000921.1 8.70e-03 35 77NC_000921.1 7.67e-01 35 78NC_000921.1 9.10e-05 1_[1(3.64e-06)]_23 79NC_000921.1 9.10e-05 1_[1(3.64e-06)]_23 80NC_000921.1 7.28e-01 35 81NC_000921.1 1.53e-01 35 82NC_000921.1 9.34e-01 35 83NC_000921.1 4.03e-02 35 84NC_000921.1 6.52e-02 35 85NC_000921.1 8.51e-01 35 86NC_000921.1 7.72e-01 35 87NC_000921.1 6.87e-01 35 88NC_000921.1 8.92e-01 35 89NC_000921.1 1.36e-02 35 90NC_000921.1 3.03e-01 35 91NC_000921.1 2.20e-01 35 92NC_000921.1 5.15e-01 35 93NC_000921.1 3.97e-01 35 94NC_000921.1 3.56e-01 35 95NC_000921.1 4.22e-01 35 96NC_000921.1 8.98e-02 35 97NC_000921.1 6.90e-02 35 98NC_000921.1 4.06e-01 35 99NC_000921.1 3.89e-01 35 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************