I've used both exonerate affine:local and needleall for pairwise alignment, but preferably using exonerate as it allow me to perform batch local pairwise alignments.

Using exonerate, with the --ryo option, I was able to generate my desired output format. But, there's one thing that has been bothering me which is the percentage identity. When aligning 2 sequences, only the sequence identity but not the sequence gaps was taken into account of the percentage identity.

For instance, using exonerate, a gap in between 129 to191bp was observed but the percentage identity still showed 100% identity (underlined in red).

Unlike the output from needleall where the gap will be taken into consideration and the percentage identity would fallen to 99.5% identity.

I would still like to stuck with exonerate for my pairwise alignment but can anyone suggest me on how to make sure the gap will also be included into the identity percentage?