I am locating specific sequences in a genome using BlastN. The sequences (47 nucleotides of total length) include (after a filtering process) 32 original nucleotides and 15 bases of a sequence that does not appear in the genome coming from a transposon insertion.
My intention is to give to blast the condition that it has to be 32 nucleotides matching the genome in the same alignment block. I do not find this concrete option but maybe an expert in blast could achieve the same results playing with the open and extension gap costs.
Thank you very much in advance.