******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.1 (Release date: Wed Mar 25 11:40:43 2015 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . 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-suite.org . ******************************************************************************** ******************************************************************************** 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= MEME02.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ codB 1.0000 100 purE 1.0000 100 pyrC 1.0000 100 purR 1.0000 100 cvpA 1.0000 100 purM 1.0000 100 guaB 1.0000 100 glnB 1.0000 100 purL 1.0000 100 purA 1.0000 100 folD 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 MEME02.fasta -dna -oc . -nostatus -time 18000 -maxsize 60000 -mod zoops -nmotifs 1 -minw 16 -maxw 16 -revcomp model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 16 maxw= 16 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 11 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= 1100 N= 11 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.275 C 0.225 G 0.225 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.225 G 0.225 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 11 llr = 154 E-value = 5.4e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a4:39a7::1::4:12 pos.-specific C :1:71::a::::1912 probability G :39:::::95:13:7: matrix T :31:::3:15a93116 bits 2.2 * 1.9 * * * * 1.7 * * * ** * * 1.5 * * ** ** ** * Relative 1.3 * **** ** ** * Entropy 1.1 * ******* ** * (20.2 bits) 0.9 * ******* ** ** 0.6 * ********** *** 0.4 * ********** *** 0.2 * ********** *** 0.0 ---------------- Multilevel AAGCAAACGGTTACGT consensus G A T T G sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------- purE - 14 1.14e-08 AAAGAGAGCA AGGAAAACGGTTGCGT GGCTGTGAAA purL + 9 1.70e-08 TTATTTCC ACGCAAACGGTTTCGT CAGCGCATCA purM - 21 1.70e-08 CTAACAGGGA AAGCAAACGTTTGCGA GACTGCTTTA cvpA - 29 1.70e-08 CTAACAGAAA AAGAAAACGTTTGCGT AGGGATTTCC codB - 18 1.96e-08 TGAAGATAAA AAGCAATCGTTTTCGT GGGGAAATAT guaB + 32 4.34e-08 AAAGGGGTAG ATGCAATCGGTTACGC TCTGTATAAT purR + 40 4.34e-08 AGGTGTGTAA AGGCAAACGTTTACCT TGCGATTTTG pyrC + 34 2.08e-07 TTTCGTGCAA AGGAAAACGTTTCCGC TTATCCTTTG glnB + 18 1.30e-06 CACGAGCTGG ATGCAAACGATTTCAA GGAATGAATT purA + 78 2.19e-06 ATCCATTTTT AAGCAAACGGTGATTT TGAAAAA folD - 75 5.01e-06 CAGAGAGAGG ATTCCATCTGTTACGT AGATCGAAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- purE 1.1e-08 13_[-1]_71 purL 1.7e-08 8_[+1]_76 purM 1.7e-08 20_[-1]_64 cvpA 1.7e-08 28_[-1]_56 codB 2e-08 17_[-1]_67 guaB 4.3e-08 31_[+1]_53 purR 4.3e-08 39_[+1]_45 pyrC 2.1e-07 33_[+1]_51 glnB 1.3e-06 17_[+1]_67 purA 2.2e-06 77_[+1]_7 folD 5e-06 74_[-1]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=11 purE ( 14) AGGAAAACGGTTGCGT 1 purL ( 9) ACGCAAACGGTTTCGT 1 purM ( 21) AAGCAAACGTTTGCGA 1 cvpA ( 29) AAGAAAACGTTTGCGT 1 codB ( 18) AAGCAATCGTTTTCGT 1 guaB ( 32) ATGCAATCGGTTACGC 1 purR ( 40) AGGCAAACGTTTACCT 1 pyrC ( 34) AGGAAAACGTTTCCGC 1 glnB ( 18) ATGCAAACGATTTCAA 1 purA ( 78) AAGCAAACGGTGATTT 1 folD ( 75) ATTCCATCTGTTACGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 935 bayes= 6.39232 E= 5.4e-016 186 -1010 -1010 -1010 40 -131 28 -1 -1010 -1010 201 -159 -1 169 -1010 -1010 172 -131 -1010 -1010 186 -1010 -1010 -1010 140 -1010 -1010 -1 -1010 215 -1010 -1010 -1010 -1010 201 -159 -159 -1010 101 72 -1010 -1010 -1010 186 -1010 -1010 -131 172 40 -131 28 -1 -1010 201 -1010 -159 -159 -131 169 -159 -60 -31 -1010 121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 5.4e-016 1.000000 0.000000 0.000000 0.000000 0.363636 0.090909 0.272727 0.272727 0.000000 0.000000 0.909091 0.090909 0.272727 0.727273 0.000000 0.000000 0.909091 0.090909 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.727273 0.000000 0.000000 0.272727 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.909091 0.090909 0.090909 0.000000 0.454545 0.454545 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.090909 0.909091 0.363636 0.090909 0.272727 0.272727 0.000000 0.909091 0.000000 0.090909 0.090909 0.090909 0.727273 0.090909 0.181818 0.181818 0.000000 0.636364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[AGT]G[CA]AA[AT]CG[GT]TT[AGT]CGT -------------------------------------------------------------------------------- Time 0.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- codB 3.34e-06 17_[-1(1.96e-08)]_67 purE 1.94e-06 13_[-1(1.14e-08)]_71 pyrC 3.54e-05 33_[+1(2.08e-07)]_51 purR 7.37e-06 39_[+1(4.34e-08)]_45 cvpA 2.89e-06 28_[-1(1.70e-08)]_56 purM 2.89e-06 20_[-1(1.70e-08)]_64 guaB 7.37e-06 31_[+1(4.34e-08)]_53 glnB 2.20e-04 17_[+1(1.30e-06)]_67 purL 2.89e-06 8_[+1(1.70e-08)]_76 purA 3.72e-04 77_[+1(2.19e-06)]_7 folD 8.51e-04 74_[-1(5.01e-06)]_10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: meme-server ********************************************************************************