<p>I find the way to get the identity of hsp ,but no alignment.One alignment can have multiple hsp, that means the score(identity) of hsp is no equal to alignment. when i do blast in webpage, i always get scores and identities of alignments. Is that any logical problem i made, who can explain this?</p>

<p>BLAST is a local alignment tool - it reports segments of the sequence, called HSPs, that align and produce the best scores. Each HSP in a match is a segment of query matching to a segment of the subject producing a high score. You can either use the meaningful maximum score or use a score totaled across all HSPs.</p>

<p>BLAST web UI has the same option - for identity percentage in case of multiple HSPs, it gives you the minimum identity% of the HSPs.</p>
