******************************************************************************** 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= motiv_ecoli/meme.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ guaB 1.0000 100 guaA 1.0000 100 purB 1.0000 100 purR 1.0000 100 purL 1.0000 100 purF 1.0000 100 purN 1.0000 100 purA 1.0000 100 purT 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 motiv_ecoli/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc motiv_ecoli/ 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= 9 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= 900 N= 9 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.224 G 0.224 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.224 G 0.224 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 6 llr = 83 E-value = 3.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a2::8a8:::::7 pos.-specific C :3:a2::a::::: probability G :2a:::::a7:3: matrix T :3::::2::3a73 bits 2.2 ** ** 1.9 * ** * ** * 1.7 * ** * ** * 1.5 * ** * ** * Relative 1.3 * ******* * Entropy 1.1 * ********** (19.9 bits) 0.9 * *********** 0.6 * *********** 0.4 * *********** 0.2 * *********** 0.0 ------------- Multilevel ACGCAAACGGTTA consensus T T GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- purL + 9 9.31e-08 TTATTTCC ACGCAAACGGTTT CGTCAGCGCA purA + 79 2.14e-07 ATCCATTTTT AAGCAAACGGTGA TTTTGAAAA purT + 48 3.79e-07 ATAAAGACAC ACGCAAACGTTTT CGTTTATACT purR + 41 3.79e-07 AGGTGTGTAA AGGCAAACGTTTA CCTTGCGATT guaB + 32 4.22e-07 AAAGGGGTAG ATGCAATCGGTTA CGCTCTGTAT purN + 25 5.64e-07 GCCCTGCTCA ATGCCAACGGTGA AAACGCGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purL 9.3e-08 8_[+1]_79 purA 2.1e-07 78_[+1]_9 purT 3.8e-07 47_[+1]_40 purR 3.8e-07 40_[+1]_47 guaB 4.2e-07 31_[+1]_56 purN 5.6e-07 24_[+1]_63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=6 purL ( 9) ACGCAAACGGTTT 1 purA ( 79) AAGCAAACGGTGA 1 purT ( 48) ACGCAAACGTTTT 1 purR ( 41) AGGCAAACGTTTA 1 guaB ( 32) ATGCAATCGGTTA 1 purN ( 25) ATGCCAACGGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 792 bayes= 8.13882 E= 3.2e-002 186 -923 -923 -923 -73 57 -43 27 -923 -923 216 -923 -923 216 -923 -923 159 -43 -923 -923 186 -923 -923 -923 159 -923 -923 -73 -923 216 -923 -923 -923 -923 216 -923 -923 -923 157 27 -923 -923 -923 186 -923 -923 57 127 127 -923 -923 27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 6 E= 3.2e-002 1.000000 0.000000 0.000000 0.000000 0.166667 0.333333 0.166667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.666667 0.000000 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[CT]GCAAACG[GT]T[TG][AT] -------------------------------------------------------------------------------- Time 0.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 14 sites = 9 llr = 96 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3a62927:12:2: pos.-specific C :7::8:1:::4::: probability G 8:::::7227:111 matrix T 2::4:1:1823979 bits 2.2 1.9 * 1.7 * 1.5 * Relative 1.3 * * ** * * Entropy 1.1 *** ** * * * (15.3 bits) 0.9 ******* ** * * 0.6 ********** *** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel GCAACAGATGCTTT consensus TA TA AGGTT A sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------- purL + 29 1.12e-07 TTTCGTCAGC GCATCAGATTCTTT ATAATGACGC purN - 63 3.35e-07 GCGTTGTTCG GAATCAGAGGCTTT GATGATACCG purF + 6 3.35e-07 TTTTA TCATCAGATGTTTT TTTGATTATC purB + 22 6.18e-07 GCGGACGTCT GCAACTGATGTTTT CTCGTAATCG guaB - 6 7.40e-06 ACCCCTTTTT GCAAAAAATGCTTG CTATC guaA - 65 9.99e-06 CGAGGCAAGT GAAACAGATAATAT AAATCGCCCG purA + 32 1.24e-05 ATTTTTGAGT GCAAAAAGTGCTGT AACTCTGAAA purT + 82 3.53e-05 CGCGCGGAAT TAATCAGGGGATAT TCGTT purR + 10 5.80e-05 CGGCGTACC GCAACACTTTTGTT GTGCGTAAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purL 1.1e-07 28_[+2]_58 purN 3.3e-07 62_[-2]_24 purF 3.3e-07 5_[+2]_81 purB 6.2e-07 21_[+2]_65 guaB 7.4e-06 5_[-2]_81 guaA 1e-05 64_[-2]_22 purA 1.2e-05 31_[+2]_55 purT 3.5e-05 81_[+2]_5 purR 5.8e-05 9_[+2]_77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=9 purL ( 29) GCATCAGATTCTTT 1 purN ( 63) GAATCAGAGGCTTT 1 purF ( 6) TCATCAGATGTTTT 1 purB ( 22) GCAACTGATGTTTT 1 guaB ( 6) GCAAAAAATGCTTG 1 guaA ( 65) GAAACAGATAATAT 1 purA ( 32) GCAAAAAGTGCTGT 1 purT ( 82) TAATCAGGGGATAT 1 purR ( 10) GCAACACTTTTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 783 bayes= 6.42626 E= 1.4e+001 -982 -982 179 -31 27 157 -982 -982 186 -982 -982 -982 101 -982 -982 69 -31 179 -982 -982 169 -982 -982 -131 -31 -101 157 -982 127 -982 -1 -131 -982 -982 -1 149 -131 -982 157 -31 -31 99 -982 27 -982 -982 -101 169 -31 -982 -101 127 -982 -982 -101 169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 9 E= 1.4e+001 0.000000 0.000000 0.777778 0.222222 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.444444 0.222222 0.777778 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.222222 0.111111 0.666667 0.000000 0.666667 0.000000 0.222222 0.111111 0.000000 0.000000 0.222222 0.777778 0.111111 0.000000 0.666667 0.222222 0.222222 0.444444 0.000000 0.333333 0.000000 0.000000 0.111111 0.888889 0.222222 0.000000 0.111111 0.666667 0.000000 0.000000 0.111111 0.888889 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][CA]A[AT][CA]A[GA][AG][TG][GT][CTA]T[TA]T -------------------------------------------------------------------------------- Time 0.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 15 sites = 7 llr = 83 E-value = 2.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :4111:37:4171:1 pos.-specific C 7::::a:::3:33:: probability G 3:793:73a36:::1 matrix T :61:6:::::3:6a7 bits 2.2 * * 1.9 * * * 1.7 * * * 1.5 * * * * Relative 1.3 * * ** * * Entropy 1.1 * * **** * * (17.2 bits) 0.9 **** **** * * 0.6 ********* ***** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CTGGTCGAGAGATTT consensus GA G AG CTCC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- purN - 6 8.80e-08 TGGCATTGAG CAGGGCGAGGGCTTT GTCCA guaB + 83 2.02e-07 ATTAACCACT CTGGTCGAGATATTG CCC guaA + 50 7.09e-07 CGCCCGACTT CATGTCGGGCGATTT ATATTATCTG purF - 43 1.51e-06 CACTTACGCT CTGGGCAAGAAACTT GACGAGCTTT purB - 40 3.86e-06 TTTTGCCTGA GTGGTCAGGCGATTA CGAGAAAACA purL + 86 4.70e-06 CGAAAGCTTA GAAGACGAGAGACTT purA + 10 5.83e-06 AAAAACAGA CTGATCGAGGTCATT TTTGAGTGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purN 8.8e-08 5_[-3]_80 guaB 2e-07 82_[+3]_3 guaA 7.1e-07 49_[+3]_36 purF 1.5e-06 42_[-3]_43 purB 3.9e-06 39_[-3]_46 purL 4.7e-06 85_[+3] purA 5.8e-06 9_[+3]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=7 purN ( 6) CAGGGCGAGGGCTTT 1 guaB ( 83) CTGGTCGAGATATTG 1 guaA ( 50) CATGTCGGGCGATTT 1 purF ( 43) CTGGGCAAGAAACTT 1 purB ( 40) GTGGTCAGGCGATTA 1 purL ( 86) GAAGACGAGAGACTT 1 purA ( 10) CTGATCGAGGTCATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 774 bayes= 6.6181 E= 2.0e+003 -945 167 35 -945 63 -945 -945 105 -95 -945 167 -95 -95 -945 193 -945 -95 -945 35 105 -945 216 -945 -945 5 -945 167 -945 137 -945 35 -945 -945 -945 216 -945 63 35 35 -945 -95 -945 135 5 137 35 -945 -945 -95 35 -945 105 -945 -945 -945 186 -95 -945 -65 137 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 2.0e+003 0.000000 0.714286 0.285714 0.000000 0.428571 0.000000 0.000000 0.571429 0.142857 0.000000 0.714286 0.142857 0.142857 0.000000 0.857143 0.000000 0.142857 0.000000 0.285714 0.571429 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.714286 0.000000 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.285714 0.285714 0.000000 0.142857 0.000000 0.571429 0.285714 0.714286 0.285714 0.000000 0.000000 0.142857 0.285714 0.000000 0.571429 0.000000 0.000000 0.000000 1.000000 0.142857 0.000000 0.142857 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][TA]GG[TG]C[GA][AG]G[ACG][GT][AC][TC]TT -------------------------------------------------------------------------------- Time 1.18 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- guaB 1.25e-09 5_[-2(7.40e-06)]_12_[+1(4.22e-07)]_38_[+3(2.02e-07)]_3 guaA 2.29e-05 49_[+3(7.09e-07)]_[-2(9.99e-06)]_22 purB 6.44e-06 21_[+2(6.18e-07)]_4_[-3(3.86e-06)]_46 purR 4.95e-05 9_[+2(5.80e-05)]_17_[+1(3.79e-07)]_47 purL 1.16e-10 8_[+1(9.31e-08)]_7_[+2(1.12e-07)]_43_[+3(4.70e-06)] purF 2.47e-06 5_[+2(3.35e-07)]_23_[-3(1.51e-06)]_43 purN 4.23e-11 5_[-3(8.80e-08)]_4_[+1(5.64e-07)]_25_[-2(3.35e-07)]_24 purA 2.39e-08 9_[+3(5.83e-06)]_7_[+2(1.24e-05)]_33_[+1(2.14e-07)]_9 purT 1.14e-05 47_[+1(3.79e-07)]_21_[+2(3.53e-05)]_5 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************