I have two DNA sequences and I am interested in finding long stretches of DNA that these two sequences share. I prefer long stretches (up to 500 kb) with lower identity (> 85 %) rather than many shorter, perfect hits. Which programs and parameters would you recommend?
I started with blastn and tried to use as lenient parameters as I could, resulting in
blastn -db db.fasta -query query.fasta -outfmt 7 -gapopen 2 -gapextend 1 -penalty -1 -num_threads 30 -perc_identity 85 -word_size 20
but I still clearly see "breaks" in alignments, suggesting that the alignment extension is stopped before it hits new region with high identity. What else could I try? Still, I want my overall alignment to have at least 85 % identity.