Recently I used NCBI blastp with an AA sequence; the resulting report contained multiple hits in the description field separated by ">" with those hits clearly shown in the alignments section:
followed by alignments involving the query sequence and the HSPs related only with the first hit (gi|1...).
What are gi|2, gi|3?
I thought they were hits with the same evalue and score of the first hit gi|1. However, it doesn't seem so since looking at the hit list you can find hits with the same evalue and score appearing on different lines.
Thanks for any help.