I'd like to compare my own BLAST tool with NCBI blast+ tool but couldn't find the default parameter of this version. I'd like to know the scoring scheme for match, mismatch, opening gap and extended gap.
I've created a NCBI blast+ output and it prints at the end of the file:
Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5
For the first line assume that for match 1 and for mismatch -2 is used. and for opening gap they used 0 and for extension gap 2.5?