I would need to perform BLAST to provide individual blast results (non-truncated alignments) for some primers and probes with potential cross-reacting organisms. Specifically, I would need the percent sequence homology for each organism relative to the target analyte primers/probes in my test. My problem is that the program not aligns the complete sequence of the primer (i.e.21 nt), but a shorter fragment (i.e. 7 nt). This way, the % homology obtained is higher than real. There are some algorithm parameters that I could change to improve the search? I would really appreciate your help.