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Old 11-05-2013, 01:06 AM   #2
Location: San Francisco, CA

Join Date: Mar 2012
Posts: 21

-n mode only considers mismatches in part of the read sequence (in the seed). Also, it takes the base quality scores into account when deciding what is the best alignment.
(See point 2. here)

-v 0 is right for finding exact matches.
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