[Bioperl-l] blasting two identical seq yields only 88% identity

[Anders Stegmann]

Merry christmas BioPerl!

I obtained some odd result blasting a protein sequence against
a chromosome I new encoded the protein using tblastn. 
So I tested the problem by blasting the protein against a database only containing the exact same protein sequence using blastp (both files were fasta formated).
I obtained an identity of only 88% instead of 100%? A lot of X'ses were incorporated in the query sequence.

I figured that it had something to do with the database formatting so I tried several possibilities with no luck
(First I tried: formatdb -i SSD1pDB.txt -p T -o F).

I have had this problem before blasting nucleotides.
What can I do about it?

Regards Anders.