Hi, Phil! > Score = 1815 bits (4702), Expect = 0.0 > Identities = 913/953 (95%), Positives = 913/953 (95%) > > LTLDRLSNTLSGGESQRISLATQXXXXXXXXXXXXDEPSIGLHQ (Query) > LTLDRLSNTLSGGESQRISLATQ DEPSIGLHQ > LTLDRLSNTLSGGESQRISLATQLGSSLVGSLYVLDEPSIGLHQ (Subject) > > Is there a way to make this 100%. I want to run the 2000 genes against > another genome to find 100% similar regions, 95% similar regions and > so on. Blast is filtering the query for regions of low complexity. That is why you get Xs. Turn the filter of. Cheers, Michael.