Last night I did the first reading-frame analysis of USS consensuses, but only the forward three frames because I wanted to create reverse-complement sequence sets to search for the reverse three reading frames (I made the sets and ran the searches overnight). The results were interesting (yes, frame affects the consensus) but not shocking.
This morning I did the first combined analysis of all the USS in the intergenic regions. That showed more dramatic differences from the usual whole-genome consensus but I'm not sure how solid the result is, because I had only one compatible pair of forward and reverse-complement results, and both were skewed to the left of the usual motif. I have lots of results, but the forward searches almost always find a differently-centered motif than the reverse searches, so the results can't properly be compared. So I've queue'd more searches, hoping I can
This morning I thought I had plenty of results to analyze the reverse frames, until I discovered that I'd made an error in one of sequence sets (pasted in duplicates of about 100 gene sequences). So I fixed that sequence set and the searches are running again.
I also used the forward-gene and intergenic results I have to look for covariation between different USS positions in these specialized sets - nothing striking turned up.
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