Blast Indel Calibration

Question

[Richard]

Hopefully an easy one for blast users...

My command: blastn.exe -query query1.fa -subject subject.fa -outfmt 5

My best hit ( as determined by the lowest expectation value ) contains the following:

CCCGGCCAGGCCCCCAGACTGCTGATCTAC-G-G-C-GC--CAGGGCCACCGGCATCCCC
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CCCGGCCAGGCCCCCAGACTGCTGATCTACGGCGCCAGCAGCAGGGCCACCGGCATCCCC

where my query is on the top. Perhaps you can spot what the question will be already. Although this alignment isn't incorrect, there is an alternate solution that contains just one 6 base deletion. Can anyone point me to a parameter I can use to get just one larger deletion in place of many small deletions?

Answer 1

[Richard]

Looks like all I needed was "-task blastn". By default it uses megablast.