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Old 08-26-2014, 05:04 PM   #1
Alex Lee
Junior Member
 
Location: N. Cal

Join Date: Apr 2014
Posts: 10
Default BLAT settings to match is continuously on reference?

HI I have 100 bp sequences I would like to match against a reference region. Is there a way I can set BLAT so that the match (eg 80%) is continuous? For example what I don't want is for the the first 50 bp to match then follow by X amount of bp from the reference region then match again for the last 50 bp. In other words I would like to the ability to set X, for example no more than 2 bp.

in short I would like to be able to set how many N's are betwen the two matches: match NNNNNN match

hope this is clear and someone can help. Thanks!
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blast, blat, match position, query coverage

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