Figure 2

Schematics of the probe evaluation within selection windows. A) Collection of all qualified probe sequences within each window. All probe properties are collected for every probe sequence that starts within the same selection window. Probes closer than minimal distance to existing selected probes are excluded and windows containing already selected probes due to repeated sequences are omitted. B) Selection of the highest quality probe within the window. Screening for the best probe within each selection window starts in the order of cross-hybridization level 1 through 4. Probe sequences of the same level are evaluated based on the following criteria: deviance from median Tm; probe self-annealing; BLAST percentage identity and identity stretch; and, probe length and position.