In the documentation the mismatch reporting format says:
the offset is 1 based position of difference relative to the 'Aligned Offset'
It seems the offset is the position of the mismatch in the target sequence relative to the aligned offset position. Does this not mean that multiple adjacent insertions into the query sequence are not representable?
This is impossible to represent in the mismatch format described, is it not? I tried aligning a test sequence and it seems to me novoalign will not return a match with 2 inserted bases in the query.