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primer3 - select primer in 3' end (Mar/25/2004 )


Does anyone know if there is a parameter in primer3 that I can set to search only the last 750 bp of my input sequence?

Thanks in advance,



Yes, you can.

There are two parameters you can use to ask primer3 to only pick primers in the last 750 bp of your sequence.

1) target region: you give for example "800,10" which means the sequence from 800-810 must be included in your PCR product.

2) Included region: you give for example "750, 500" which means the primers must be pick within 750-800 bp region.

Or you can simply paste only the last part of your sequence into the program.

Help it helps.



Thanks for the reply,

Is there a way to set the parameter in target region as ‘750 bp from the last base’, such as –750? I’m loading a file with multiple sequences – each sequence is a different length- and would rather not pull out the last 750 bp from each sequence.

Thanks again,

Attached File


To my knowledge, unfortunately, primer3 doesn't provide such feature. It counts position all from the begining. I understand you are doing batch processing. One thing you may want to try is to reverse complement your sequences and then specify the first 750 bp as included region.