I've been trying to design a primer from the 16S gene sequence of leptospira, to detect any species of leptospira in the isolate ( as the 16S gene sequence is highly conserved ) and BLASTing the primers that I've designed to test them. The problem with the BLAST results I get is that of the 100 hits that displayed, a good number of them are repeats. For example, a hit with the whole genome shotgun sequence of the fiocruz strain is duplicated some 20 times ( i'm guessing that these are by different workers ). Is there any way to avoid this. In particular, it would be great if I could get at least one hit per species, and not more than five. I have no clue how to go about doing this ... any ideas ?