[Biodevelopers] Blast - exact same sequence only gives 98%

[Phil Princely]

Hi all,

I'm new here, so sorry if this is a bit of an obvious question. I've
been using blast for a while now, but am still learning. Here's my
problem:

I used formatdb to make a blast database from a text file with about
2000 genes. Everything went well, and I could query the database. But
when I input a sequence from the original text file, the result isn't
always 100%. Sometimes it comes out 98% or 95%, when it should always
be 100%. When I look at the results, I find one or more series of xs,
signifying a missing part of data. For example:

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.

Thanks

Phil P