Schematic description of the probe set design procedure. A) Target-specific sequences are first designed for all targets. Tags are then added to each TSS pair in sequence to form complete probes. B) Prior to tag allocation, each TSS pair is evaluated using selected constraints and the current acceptor scheme. Accepted TSS pairs are used to create a series of probe candidates using each valid combination of tags in turn. This procedure is stopped if an acceptable candidate is found, or when all candidates have been tested. A probe is then selected from the list of accepted or temporarily accepted candidates, using the current selector scheme.