******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ foldupstream 1.0000 101 guaaupstream 1.0000 101 puraupstream 1.0000 101 purcupstream 1.0000 101 purdupstream 1.0000 101 purhupstream 1.0000 101 purlupstream 1.0000 101 purmupstream 1.0000 101 purrupstream 1.0000 101 purtupstream 1.0000 101 ******************************************************************************** ******************************************************************************** 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= 10 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= 1010 N= 10 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.250 C 0.250 G 0.250 T 0.250 Background letter frequencies (from dataset with add-one prior applied): A 0.250 C 0.250 G 0.250 T 0.250 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 8 llr = 92 E-value = 4.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 985::1::::::6 pos.-specific C 1348:3:::a35: probability G ::1:a1:3a:6:4 matrix T :::3:5a8::15: bits 2.0 * * ** 1.8 * * ** 1.6 * * ** 1.4 * * * ** Relative 1.2 ** ** **** Entropy 1.0 ** ** **** ** (16.6 bits) 0.8 ** ** ******* 0.6 ***** ******* 0.4 ***** ******* 0.2 ************* 0.0 ------------- Multilevel AAACGTTTGCGCA consensus CCT C G CTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- purhupstream + 79 2.98e-08 ATTGTAACGA AAACGTTTGCGCA ACGCTCGCGA purrupstream + 55 2.09e-07 AACGCCAGGT AAACGTTTGCCTA CACACACCCT purcupstream + 58 2.98e-07 GTACCGACGC ACACGTTTGCGTA TCTTATCAGA foldupstream - 50 5.96e-07 ATTGACGGTA AAACGATTGCGCA GCAGGTGCGA guaaupstream - 16 5.16e-06 CAGTACACTC AACTGGTTGCGCG CCGCGTGCGT purlupstream - 40 6.94e-06 CGTATCAATA AACTGCTGGCGCG CTTTCAGGCT puraupstream - 39 8.94e-06 TTTTCAAAAT CACCGTTTGCTTA AAAATGGATT purdupstream - 43 2.11e-05 GGACGCGAAC ACGCGCTGGCCTG GAAAGCCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purhupstream 3e-08 78_[+1]_10 purrupstream 2.1e-07 54_[+1]_34 purcupstream 3e-07 57_[+1]_31 foldupstream 6e-07 49_[-1]_39 guaaupstream 5.2e-06 15_[-1]_73 purlupstream 6.9e-06 39_[-1]_49 puraupstream 8.9e-06 38_[-1]_50 purdupstream 2.1e-05 42_[-1]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=8 purhupstream ( 79) AAACGTTTGCGCA 1 purrupstream ( 55) AAACGTTTGCCTA 1 purcupstream ( 58) ACACGTTTGCGTA 1 foldupstream ( 50) AAACGATTGCGCA 1 guaaupstream ( 16) AACTGGTTGCGCG 1 purlupstream ( 40) AACTGCTGGCGCG 1 puraupstream ( 39) CACCGTTTGCTTA 1 purdupstream ( 43) ACGCGCTGGCCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 890 bayes= 7.52683 E= 4.5e+000 180 -100 -965 -965 158 0 -965 -965 100 59 -100 -965 -965 159 -965 0 -965 -965 200 -965 -100 0 -100 100 -965 -965 -965 200 -965 -965 0 158 -965 -965 200 -965 -965 200 -965 -965 -965 0 132 -100 -965 100 -965 100 132 -965 59 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 8 E= 4.5e+000 0.875000 0.125000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.500000 0.375000 0.125000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.125000 0.250000 0.125000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.625000 0.125000 0.000000 0.500000 0.000000 0.500000 0.625000 0.000000 0.375000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[AC][AC][CT]G[TC]T[TG]GC[GC][CT][AG] -------------------------------------------------------------------------------- Time 0.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 11 sites = 8 llr = 75 E-value = 1.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 164361:::a3 pos.-specific C :3:1:3:a::: probability G 9:5613a:a:: matrix T :11:34::::8 bits 2.0 **** 1.8 **** 1.6 **** 1.4 * **** Relative 1.2 * ***** Entropy 1.0 * ***** (13.4 bits) 0.8 * * ***** 0.6 ***** ***** 0.4 ***** ***** 0.2 ***** ***** 0.0 ----------- Multilevel GAGGATGCGAT consensus CAATC A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------- guaaupstream + 57 2.38e-07 AGTCCAGAAT GAGGATGCGAT GCTTATGAAT purtupstream + 73 5.01e-06 ATTAGGAAAA GAGGTGGCGAT TGAATGCCAA purrupstream - 79 1.98e-05 CCGCAACCCT GATGTTGCGAT TAGGGTGTGT puraupstream + 13 1.98e-05 CTGTATATCT GAAAAAGCGAT GGTAGAATCC purdupstream - 57 2.17e-05 ATTGGTAACG GCGGACGCGAA CACGCGCTGG foldupstream - 39 3.17e-05 CGATTGCGCA GCAGGTGCGAT CTGAGGTTGC purcupstream - 37 6.29e-05 GCGTCGGTAC AAAAACGCGAT TTAACCGCTA purlupstream + 74 1.34e-04 AATGCAGACA GTGCAGGCGAA CCACGCAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- guaaupstream 2.4e-07 56_[+2]_34 purtupstream 5e-06 72_[+2]_18 purrupstream 2e-05 78_[-2]_12 puraupstream 2e-05 12_[+2]_78 purdupstream 2.2e-05 56_[-2]_34 foldupstream 3.2e-05 38_[-2]_52 purcupstream 6.3e-05 36_[-2]_54 purlupstream 0.00013 73_[+2]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=11 seqs=8 guaaupstream ( 57) GAGGATGCGAT 1 purtupstream ( 73) GAGGTGGCGAT 1 purrupstream ( 79) GATGTTGCGAT 1 puraupstream ( 13) GAAAAAGCGAT 1 purdupstream ( 57) GCGGACGCGAA 1 foldupstream ( 39) GCAGGTGCGAT 1 purcupstream ( 37) AAAAACGCGAT 1 purlupstream ( 74) GTGCAGGCGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 910 bayes= 7.55906 E= 1.4e+004 -100 -965 181 -965 132 0 -965 -100 58 -965 100 -100 0 -100 132 -965 132 -965 -100 0 -100 0 0 58 -965 -965 200 -965 -965 200 -965 -965 -965 -965 200 -965 200 -965 -965 -965 0 -965 -965 158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 8 E= 1.4e+004 0.125000 0.000000 0.875000 0.000000 0.625000 0.250000 0.000000 0.125000 0.375000 0.000000 0.500000 0.125000 0.250000 0.125000 0.625000 0.000000 0.625000 0.000000 0.125000 0.250000 0.125000 0.250000 0.250000 0.375000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AC][GA][GA][AT][TCG]GCGA[TA] -------------------------------------------------------------------------------- Time 1.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 8 sites = 8 llr = 63 E-value = 1.8e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::1:: pos.-specific C ::::8::a probability G 333a34a: matrix T 888::5:: bits 2.0 * ** 1.8 * ** 1.6 * ** 1.4 * ** Relative 1.2 ***** ** Entropy 1.0 ***** ** (11.4 bits) 0.8 ***** ** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTTGCTGC consensus GGG GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- foldupstream + 77 1.53e-05 GTCAATAATC TTTGCTGC CATCAGAGAG purhupstream + 58 3.05e-05 GTATTCTCAT TTTGCGGC GACATTGTAA purtupstream - 28 9.16e-05 CATCACTCGC GTTGCTGC CGGACGCAGC purrupstream + 93 1.53e-04 CAACATCAGG GTTGCGGC A purdupstream + 31 1.53e-04 CAGCGGCGAC TGTGCGGC TTTCCAGGCC purcupstream + 15 2.59e-04 GGCCTGTAAT TGTGGTGC GAAATAGCGG puraupstream - 87 2.59e-04 CACCCCA TTGGGTGC CCAGTACGAC purlupstream + 25 4.12e-04 GACCTGGAGG TTGGCAGC CTGAAAGCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- foldupstream 1.5e-05 76_[+3]_17 purhupstream 3.1e-05 57_[+3]_36 purtupstream 9.2e-05 27_[-3]_66 purrupstream 0.00015 92_[+3]_1 purdupstream 0.00015 30_[+3]_63 purcupstream 0.00026 14_[+3]_79 puraupstream 0.00026 86_[-3]_7 purlupstream 0.00041 24_[+3]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=8 seqs=8 foldupstream ( 77) TTTGCTGC 1 purhupstream ( 58) TTTGCGGC 1 purtupstream ( 28) GTTGCTGC 1 purrupstream ( 93) GTTGCGGC 1 purdupstream ( 31) TGTGCGGC 1 purcupstream ( 15) TGTGGTGC 1 puraupstream ( 87) TTGGGTGC 1 purlupstream ( 25) TTGGCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 940 bayes= 6.59867 E= 1.8e+005 -965 -965 0 158 -965 -965 0 158 -965 -965 0 158 -965 -965 200 -965 -965 159 0 -965 -100 -965 59 100 -965 -965 200 -965 -965 200 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 1.8e+005 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.125000 0.000000 0.375000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG][TG][TG]G[CG][TG]GC -------------------------------------------------------------------------------- Time 1.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- foldupstream 3.93e-07 38_[-2(3.17e-05)]_[-1(5.96e-07)]_14_[+3(1.53e-05)]_17 guaaupstream 6.15e-06 15_[-1(5.16e-06)]_28_[+2(2.38e-07)]_34 puraupstream 3.55e-05 12_[+2(1.98e-05)]_15_[-1(8.94e-06)]_50 purcupstream 4.86e-06 36_[-2(6.29e-05)]_10_[+1(2.98e-07)]_31 purdupstream 5.17e-05 42_[-1(2.11e-05)]_1_[-2(2.17e-05)]_34 purhupstream 3.22e-06 57_[+3(3.05e-05)]_13_[+1(2.98e-08)]_10 purlupstream 2.20e-04 39_[-1(6.94e-06)]_49 purmupstream 9.23e-01 101 purrupstream 7.87e-07 54_[+1(2.09e-07)]_11_[-2(1.98e-05)]_12 purtupstream 4.38e-04 27_[-3(9.16e-05)]_37_[+2(5.01e-06)]_18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************