Not all the Gibbs motif searches I'd queue'd ran (of course). More mysterious symbols unexpectedly hidden in sequence files, and one set of sequence files turned out to be much too long. I think this latter weirdness arose because the "splitsequence.pl" program we wrote doesn't overwrite a previous version of the specified output file (as I had assumed) but instead just adds the new sequence to whatever was in the previous version. Now I think about it, I should have realized this...
And for some reason the searches on the forward strand of the H. somnus sequence had a very hard time finding the USS pattern, even though the core motif should be obvious. But the reverse-strand searches didn't have much problem, and both forward and reverse searches found about the same number of sites. I guess this is due to some minor difference in the sites, something that just pushes the Gibbs results below the threshold of not finding ANY motifs in 100 searches.
But the last few are queue'd, and I've analyzed almost all of the ones that are finished.
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