I have two sequences, say AAAGCTCGAGG and AAAGCGAGG. I need a convenient tool which shows me insertions or deletions between these, i.e. in this case something like
AAAGCTCGAGG ||||| |||| AAAGC GAGG 2bp deletion starting at base pair 5
and also insertions such as
AAAGCTC GAGG ||||||| |||| AAAGCTCTGAGG 1bp insertion at base pair 7
Does something like that exist? Blastn finds the alignment of course, but only outputs the number of gaps, not their position. I guess I could parse a pileup, but do not want to create a bam file from one of the sequences first, so samtools seems to be out. Any further ideas?