******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ folD 1.0000 100 guaA 1.0000 100 guaB 1.0000 100 purA 1.0000 100 purD 1.0000 100 purF 1.0000 100 purK 1.0000 100 purL 1.0000 100 ******************************************************************************** ******************************************************************************** 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 -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc ./ model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 8 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= 800 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.340 C 0.160 G 0.160 T 0.340 Background letter frequencies (from dataset with add-one prior applied): A 0.340 C 0.160 G 0.160 T 0.340 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 7 llr = 80 E-value = 1.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7::::91:1: pos.-specific C :9a1919::: probability G 3::9:::::: matrix T :1::1::a9a bits 2.6 * 2.4 * 2.1 ** 1.8 **** * Relative 1.6 **** ** * Entropy 1.3 **** ** * (16.6 bits) 1.1 ********** 0.8 ********** 0.5 ********** 0.3 ********** 0.0 ---------- Multilevel ACCGCACTTT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- purK + 49 4.76e-07 TTTAGATCTG ACCGCACTTT TGAAGTGCGG purF + 6 4.76e-07 TTAAT ACCGCACTTT GGTTTTATTA purA + 3 4.76e-07 TC ACCGCACTTT TTCTTTTTAT guaA - 28 4.76e-07 GCAAAAACCA ACCGCACTTT AAACAGCAAA purD + 60 6.90e-06 GTAAAAAATA GCCGTACTTT TTTTAAATTA guaB + 60 1.93e-05 GTATAATCCC GCCGCAATAT TTTTTAACTT folD + 15 3.20e-05 TTTAAGAAAT ATCCCCCTTT TTCATTGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purK 4.8e-07 48_[+1]_42 purF 4.8e-07 5_[+1]_85 purA 4.8e-07 2_[+1]_88 guaA 4.8e-07 27_[-1]_63 purD 6.9e-06 59_[+1]_31 guaB 1.9e-05 59_[+1]_31 folD 3.2e-05 14_[+1]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=7 purK ( 49) ACCGCACTTT 1 purF ( 6) ACCGCACTTT 1 purA ( 3) ACCGCACTTT 1 guaA ( 28) ACCGCACTTT 1 purD ( 60) GCCGTACTTT 1 guaB ( 60) GCCGCAATAT 1 folD ( 15) ATCCCCCTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 728 bayes= 7.29702 E= 1.0e-003 107 -945 83 -945 -945 242 -945 -125 -945 264 -945 -945 -945 -17 242 -945 -945 242 -945 -125 133 -17 -945 -945 -125 242 -945 -945 -945 -945 -945 156 -125 -945 -945 133 -945 -945 -945 156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 1.0e-003 0.714286 0.000000 0.285714 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.857143 0.000000 0.142857 0.857143 0.142857 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG]CCGCACTTT -------------------------------------------------------------------------------- Time 0.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 9 sites = 8 llr = 67 E-value = 9.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 11::1:31: pos.-specific C 39:::::81 probability G 6:81:18:: matrix T ::3999:19 bits 2.6 2.4 2.1 1.8 * Relative 1.6 ** * Entropy 1.3 *** ** (12.1 bits) 1.1 ********* 0.8 ********* 0.5 ********* 0.3 ********* 0.0 --------- Multilevel GCGTTTGCT consensus C T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------- folD - 57 1.40e-06 GAAAAAGAAA GCGTTTGCT ATTTTAACGA purL + 39 1.80e-05 TTGAATGCAA ACGTTTGCT TTGTTCGTTA purA - 51 3.29e-05 AAATAAACAG CCGTTTACT TTACTCTTTT guaA + 15 3.29e-05 CTTTAGCCTG CCTTTTGCT GTTTAAAGTG purD - 80 4.47e-05 TGTAGTCCTT GCGTATGCC TAATTTAAAA purK + 65 7.36e-05 CTTTTGAAGT GCGGTTGTT TTTTTCGTAA purF - 71 7.36e-05 TATTGATTAA GCGTTGGAT TTAAAAAACT guaB - 40 5.73e-04 GGATTATACA GATTTTACT TGATTTTGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- folD 1.4e-06 56_[-2]_35 purL 1.8e-05 38_[+2]_53 purA 3.3e-05 50_[-2]_41 guaA 3.3e-05 14_[+2]_77 purD 4.5e-05 79_[-2]_12 purK 7.4e-05 64_[+2]_27 purF 7.4e-05 70_[-2]_21 guaB 0.00057 39_[-2]_52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=9 seqs=8 folD ( 57) GCGTTTGCT 1 purL ( 39) ACGTTTGCT 1 purA ( 51) CCGTTTACT 1 guaA ( 15) CCTTTTGCT 1 purD ( 80) GCGTATGCC 1 purK ( 65) GCGGTTGTT 1 purF ( 71) GCGTTGGAT 1 guaB ( 40) GATTTTACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 736 bayes= 6.50779 E= 9.0e+002 -144 64 196 -965 -144 245 -965 -965 -965 -965 222 -44 -965 -965 -36 136 -144 -965 -965 136 -965 -965 -36 136 -44 -965 222 -965 -144 222 -965 -144 -965 -36 -965 136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 8 E= 9.0e+002 0.125000 0.250000 0.625000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.125000 0.875000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.875000 0.250000 0.000000 0.750000 0.000000 0.125000 0.750000 0.000000 0.125000 0.000000 0.125000 0.000000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC]C[GT]TTT[GA]CT -------------------------------------------------------------------------------- Time 0.62 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 8 sites = 2 llr = 23 E-value = 4.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a:::::aa pos.-specific C :::5:::: probability G :aa5aa:: matrix T :::::::: bits 2.6 ** ** 2.4 ** ** 2.1 ** ** 1.8 ** ** Relative 1.6 ******** Entropy 1.3 ******** (16.9 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGGCGGAA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- purD + 36 8.24e-06 TTTACAAAAG AGGGGGAA TTGCAGGTAA purA + 90 8.24e-06 ACCGAATAAA AGGCGGAA ATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purD 8.2e-06 35_[+3]_57 purA 8.2e-06 89_[+3]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=8 seqs=2 purD ( 36) AGGGGGAA 1 purA ( 90) AGGCGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 744 bayes= 8.53528 E= 4.2e+003 155 -765 -765 -765 -765 -765 263 -765 -765 -765 263 -765 -765 163 163 -765 -765 -765 263 -765 -765 -765 263 -765 155 -765 -765 -765 155 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.2e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 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 3 regular expression -------------------------------------------------------------------------------- AGG[CG]GGAA -------------------------------------------------------------------------------- Time 0.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- folD 2.81e-06 14_[+1(3.20e-05)]_32_[-2(1.40e-06)]_35 guaA 3.11e-05 14_[+2(3.29e-05)]_4_[-1(4.76e-07)]_63 guaB 1.50e-03 59_[+1(1.93e-05)]_31 purA 1.94e-07 2_[+1(4.76e-07)]_38_[-2(3.29e-05)]_30_[+3(8.24e-06)]_3 purD 2.84e-06 8_[-3(5.62e-05)]_19_[+3(8.24e-06)]_16_[+1(6.90e-06)]_10_[-2(4.47e-05)]_12 purF 8.50e-05 5_[+1(4.76e-07)]_55_[-2(7.36e-05)]_21 purK 1.23e-04 48_[+1(4.76e-07)]_1_[-1(7.21e-05)]_31 purL 3.32e-02 38_[+2(1.80e-05)]_53 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************