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Old 04-11-2013, 10:52 AM   #1
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Location: MA

Join Date: Oct 2010
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Default How to compare sequences and flanking regions

Hi everyone,
Sorry, but here comes the stupid question of the week: I want to look for similar sequences in a draft genome, and choose those with different flaking (at 3' and 5') regions (cos the genome has contig duplications all along the sequence).
So let's say, I have a group of similar seqs (ca. 200bp) and I want to check their 3' and 5' 50bp surrounds. In a total ~300 bp seqs database, is there a way to say to blast (or maybe other program) that I need to pick up the similar sequences in position 50-250 but with differences at 1-50 and 250-300?

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