They should be 21mers, be at least 25bp from start of the coding sequence and no closer than 150bp from its end. Candidates are scored based on various empirical rules (see the Broad Institute's web site for a complete list ) and then BLASTed against 2 transcriptome sets.
The goal is to find 21mers that meet specific criteria: they must be at least 25 base pairs away from the start of the coding sequence and no closer than 150 base pairs from its end. These candidates are evaluated based on empirical rules (see the Broad Institute's website for a complete list) and then compared to two transcriptome sets using BLAST.