How to filter out (organism-specific) interspersed repeats?
On the “blastn” (nucleotide-nucleotide) page there is an option to filter “Species-specific” repeats for a number of common organisms. This may be especially important if your query matches to the same or a related organism many times. To enable this, go to the “Algorithm parameters” section (at the bottom of the page), check “Species-specific repeats”, and choose the proper organism.
