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!
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!