Find indels between two short sequences 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?
Smith-Waterman is guaranteed to give you the best alignment given your choice of substitution matrix.  For a few such tiny sequences, it's what I would use.  Many implementations exist.