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 desired sequences are called 21mers, 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.  Candidates are scored based on various empirical rules (see the Broad Institute's website for a complete list) and then compared to two transcriptome sets using BLAST.