I'm aligning pairs of genomic scaffolds, looking for 1000bp-size insertions/deletions. Its easy to get a dotplot for an overview. It's also easy to find SNPs at a small-scale. But I need to find putative insertions and subsequently confirm them in the lab. Thus I need something I can open in Jalview or something else, where it is easy to see the insertions and to copy-paste the relevant sequences into something for primer design.
I can get such alignments in useable time with clustal (sorry), but not if both sequences are 1MB or bigger. Mummer is super fast, but has a weird output format. Anything else I could use that is fast but gives a user-friendly output? (BLAST would be great, but it divides the aligning bits up into multiple HSPs instead of one long contiguous alignment).