We then filtered the candidate probeset-mRNA mapping relationships by aligning probe sequences in these probesets against their corresponding transcripts. Probes were blasted against their candidate mRNA targets using the bl2seq program [61] , and the probe to transcript matches were accepted if no more than one mismatch was found. At the level of probesets, the probeset to transcript matches were accepted only if more than 90% of all probes within a probeset (over 10 probes for the typical 11-probeset) were mapped to the transcript in the same orientation.