******************************************************************************** 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_pr5/meme.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ purE 1.0000 101 purT 1.0000 101 purA 1.0000 101 purL 1.0000 101 folD 1.0000 101 purD 1.0000 101 purK 1.0000 101 purM 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_pr5/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc meme_pr5/ 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= 808 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from dataset with add-one prior applied): A 0.304 C 0.196 G 0.196 T 0.304 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 23 sites = 5 llr = 138 E-value = 1.3e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A aa4a622a:a2::aaa::::::: pos.-specific C ::6::88:2:8:a:::a:::::a probability G ::::::::4::a:::::a:::a: matrix T ::::4:::4:::::::::aaa:: bits 2.4 ** ** ** 2.1 ** ** ** 1.9 ** ** ** 1.6 ** * * * ************ Relative 1.4 ** * *** ************** Entropy 1.2 **** *** ************** (40.0 bits) 0.9 **** *** ************** 0.7 ******** ************** 0.5 *********************** 0.2 *********************** 0.0 ----------------------- Multilevel AACAACCAGACGCAAACGTTTGC consensus A TAA T A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------------- folD - 17 7.82e-14 AATTCTAATT AACATCCATACGCAAACGTTTGC CTTGTGGTGT purL + 63 7.82e-14 AATTCTAATT AACATCCATACGCAAACGTTTGC CTTGTGGTGT purE + 5 2.33e-13 CGTC AACAACAAGACGCAAACGTTTGC TTGAGATAAA purM + 11 5.49e-13 TCACTAAAGA AAAAAACAGACGCAAACGTTTGC TATCTGTATT purT + 10 8.58e-13 TTATTGACA AAAAACCACAAGCAAACGTTTGC TTCACAATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- folD 7.8e-14 16_[-1]_62 purL 7.8e-14 62_[+1]_16 purE 2.3e-13 4_[+1]_74 purM 5.5e-13 10_[+1]_68 purT 8.6e-13 9_[+1]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=23 seqs=5 folD ( 17) AACATCCATACGCAAACGTTTGC 1 purL ( 63) AACATCCATACGCAAACGTTTGC 1 purE ( 5) AACAACAAGACGCAAACGTTTGC 1 purM ( 11) AAAAAACAGACGCAAACGTTTGC 1 purT ( 10) AAAAACCACAAGCAAACGTTTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 23 n= 632 bayes= 7.22377 E= 1.3e-014 171 -897 -897 -897 171 -897 -897 -897 39 161 -897 -897 171 -897 -897 -897 98 -897 -897 39 -60 203 -897 -897 -60 203 -897 -897 171 -897 -897 -897 -897 3 103 39 171 -897 -897 -897 -60 203 -897 -897 -897 -897 235 -897 -897 235 -897 -897 171 -897 -897 -897 171 -897 -897 -897 171 -897 -897 -897 -897 235 -897 -897 -897 -897 235 -897 -897 -897 -897 171 -897 -897 -897 171 -897 -897 -897 171 -897 -897 235 -897 -897 235 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 23 nsites= 5 E= 1.3e-014 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.200000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.400000 0.400000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AA[CA]A[AT][CA][CA]A[GTC]A[CA]GCAAACGTTTGC -------------------------------------------------------------------------------- Time 0.35 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 45 sites = 3 llr = 146 E-value = 1.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::73aaa::a7:773::77a:3a3:::::::::a::3:3::7: pos.-specific C 7a::3:::::::::::::a:::::::7::7::a:a:::::737:: probability G 3::3::::::::3a:37a::3:::::::737a:a::::7::733a matrix T ::a7:7:::aa:::3::::3::a7:73a3:3:::::aa:a::::: bits 2.4 * * ** **** * 2.1 * * ** **** * 1.9 * * ** **** * 1.6 ** ****** * ** ** * * ******* * * Relative 1.4 *** ****** * ** ** * * * ******* * ** * Entropy 1.2 *** ****** * *** ** * ***************** * (70.1 bits) 0.9 ***** ******** **** *** * ******************* 0.7 ********************************************* 0.5 ********************************************* 0.2 ********************************************* 0.0 --------------------------------------------- Multilevel CCTTATAAATTAAGAAGGCAAATTATCTGCGGCGCATTGTCGCAG consensus G GCA G TGA TG A AT TGT A ACGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------------------------------- folD - 51 1.28e-27 GACTTT CCTTATAAATTAAGAAGGCAAATTATCTGCGGCGCATTGTCGCAG AAATTCTAAT purL + 7 1.28e-27 GACTTT CCTTATAAATTAAGAAGGCAAATTATCTGCGGCGCATTGTCGCAG AAATTCTAAT purE - 42 1.22e-19 ACTCCTTCAA GCTGCAAAATTAGGTGAGCTGATAAATTTGTGCGCATTATACGGG GATTTTTATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- folD 1.3e-27 50_[-2]_6 purL 1.3e-27 6_[+2]_50 purE 1.2e-19 41_[-2]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=45 seqs=3 folD ( 51) CCTTATAAATTAAGAAGGCAAATTATCTGCGGCGCATTGTCGCAG 1 purL ( 7) CCTTATAAATTAAGAAGGCAAATTATCTGCGGCGCATTGTCGCAG 1 purE ( 42) GCTGCAAAATTAGGTGAGCTGATAAATTTGTGCGCATTATACGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 45 n= 456 bayes= 7.68841 E= 1.4e-002 -823 176 77 -823 -823 235 -823 -823 -823 -823 -823 171 -823 -823 77 113 113 77 -823 -823 13 -823 -823 113 171 -823 -823 -823 171 -823 -823 -823 171 -823 -823 -823 -823 -823 -823 171 -823 -823 -823 171 171 -823 -823 -823 113 -823 77 -823 -823 -823 235 -823 113 -823 -823 13 113 -823 77 -823 13 -823 176 -823 -823 -823 235 -823 -823 235 -823 -823 113 -823 -823 13 113 -823 77 -823 171 -823 -823 -823 -823 -823 -823 171 13 -823 -823 113 171 -823 -823 -823 13 -823 -823 113 -823 176 -823 13 -823 -823 -823 171 -823 -823 176 13 -823 176 77 -823 -823 -823 176 13 -823 -823 235 -823 -823 235 -823 -823 -823 -823 235 -823 -823 235 -823 -823 171 -823 -823 -823 -823 -823 -823 171 -823 -823 -823 171 13 -823 176 -823 -823 -823 -823 171 13 176 -823 -823 -823 77 176 -823 -823 176 77 -823 113 -823 77 -823 -823 -823 235 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 45 nsites= 3 E= 1.4e-002 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CG]CT[TG][AC][TA]AAATTA[AG]G[AT][AG][GA]GC[AT][AG]AT[TA]A[TA][CT]T[GT][CG][GT]GCGCATT[GA]T[CA][GC][CG][AG]G -------------------------------------------------------------------------------- Time 0.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 15 sites = 2 llr = 41 E-value = 3.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :aaaaa:a::a:aa: pos.-specific C a:::::a:aa:a::: probability G ::::::::::::::a matrix T ::::::::::::::: bits 2.4 * * ** * * 2.1 * * ** * * 1.9 * * ** * * 1.6 *************** Relative 1.4 *************** Entropy 1.2 *************** (29.6 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CAAAAACACCACAAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- folD + 2 1.26e-09 T CAAAAACACCACAAG GCAAACGTTT purL - 86 1.26e-09 T CAAAAACACCACAAG GCAAACGTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- folD 1.3e-09 1_[+3]_85 purL 1.3e-09 85_[-3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=2 folD ( 2) CAAAAACACCACAAG 1 purL ( 86) CAAAAACACCACAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 696 bayes= 8.43879 E= 3.1e+003 -765 235 -765 -765 171 -765 -765 -765 171 -765 -765 -765 171 -765 -765 -765 171 -765 -765 -765 171 -765 -765 -765 -765 235 -765 -765 171 -765 -765 -765 -765 235 -765 -765 -765 235 -765 -765 171 -765 -765 -765 -765 235 -765 -765 171 -765 -765 -765 171 -765 -765 -765 -765 -765 235 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2 E= 3.1e+003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CAAAAACACCACAAG -------------------------------------------------------------------------------- Time 0.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purE 5.46e-25 4_[+1(2.33e-13)]_14_[-2(1.22e-19)]_15 purT 2.55e-11 9_[+1(8.58e-13)]_69 purA 2.66e-01 101 purL 1.92e-39 6_[+2(1.28e-27)]_11_[+1(7.82e-14)]_[-3(1.26e-09)]_1 folD 1.92e-39 1_[+3(1.26e-09)]_[-1(7.82e-14)]_11_[-2(1.28e-27)]_6 purD 2.93e-01 101 purK 2.56e-01 101 purM 6.26e-09 10_[+1(5.49e-13)]_68 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo ********************************************************************************