MEME version 3.0 (Release date: 2002/04/02 00:11:59)
For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu.
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.sdsc.edu.
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.
DATAFILE= 71NTCA.NT ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 71C_2335094-2335693c 1.0000 600 71C_2807124-2807482d 1.0000 359 71C_704034-704678d 1.0000 645 71C_701219-701460c 1.0000 242 NC_4477940-4478869d 1.0000 930 71C_3427135-3428063d 1.0000 929
This information can also be useful in the event you wish to report a problem with the MEME software. command: meme 71NTCA.NT -nmotifs 3 -dna 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= 6 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 3705 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.328 C 0.175 G 0.174 T 0.322 Background letter frequencies (from dataset with add-one prior applied): A 0.328 C 0.176 G 0.174 T 0.322
Time 24.93 secs.
Time 48.74 secs.
Time 69.88 secs.
CPU: hercules.vcu.edu
MOTIFS
For each motif that it discovers in the training set, MEME prints the following information:
Multilevel TTATGTGAACGACGTCACACT consensus AA T A G A GA AA sequence T C TT T
You can convert these blocks to PSSMs (position-specific scoring matrices), LOGOS (color representations of the motifs), phylogeny trees and search them against a database of other blocks by pasting everything from the "BL" line to the "//" line (inclusive) into the Multiple Alignment Processor. If you include the -print_fasta switch on the command line, MEME prints the motif sites in FASTA format instead of BLOCKS format.