I'm running a local BLAST search on a HERV-K(HML2) LTR sequence in the human genome. I get thousands of hits.
I want to retrieve the hits that correspond to other HERV-K(HML2) LTR sequences only.
What alignment length/identity filters should I use on the hits to select LTRs of the same family? Insertions and deletions could easily alter the alignment lengths meaning the cutoff length for the filter I want isn't clear. I can work out what alignment length cutoffs remove what percentage of the results to identify big drops at specific cutoffs, but it hasn't been very helpful.