MAST output dropping 75-bp tiles

[CS]

Hi,

I'm trying to run MAST on some pre-aligned sequences (probably not important -- input is a standard fasta), and the output skips different 75-bp segments from my input sequences. In the HTML, these regions show up at dashes, and in the XML, these segments are skipped altogether. The same spots are reproducibly lost when I re-run MAST, and I can't figure out why. Usually each segment is lost in only one or two of my input sequences at a time.

Has this happened to anyone before?

Thanks!

[cegrant]

I suspect that FIMO may be the tool you are looking for rather than MAST.
You may find this posting on the MEME Suite Q&A site helpful:

How does MAST differ from FIMO?

The missing sequences (represented with '-' in the motif location diagram represent extended regions where there were no significant matches to any of the input motifs.