Hello,

In blastn, the output is a file that indicates parts of alignments in the two sequences. I need to know is it possible to change the output and make the alignment of parties does not aligned twice in the same position.

for example:

seq    -----|---------/---|----------/----
al1         |-------------|
al2                   /--------------/

I need to eliminate the same part in al1 and al2. And the new alignment is:

seq    -----|--------------|/----------/----
al1         |--------------|
al2                    /----/----------/

Do you have a solution?