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Old 05-18-2011, 08:13 AM   #2
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700
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This might help :
http://genome.ucsc.edu/FAQ/FAQblat.html#blat8

Please note:
http://genome.ucsc.edu/goldenPath/he...html#BLATAlign
BLAT is designed to quickly find sequences with 95% or greater similarity of length 25 bases or more

You might want to use BWA or Bowtie, instead.
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