OTV position in the probe and RFLP have significant effects on hybridization intensity and VINO detection. Left panels: probe sets are grouped by the distance from the OTV to the nearest edge of the probe sequence for each possible OTV position (either none or between 0-12). Right panels: probe sets having no evidence of an OTV within the probe sequence are grouped by the size of their smallest restriction fragment (NspI or StyI) in bins of 250 bp. Top panels show the mean intensity across each subset using the four probes for the best-hybridizing allele in each probe set for A) OTV position in the probe and B) minimum restriction fragment length. Middle panels show the number of VINO and N calls (as a percentage of all genotype calls) for probe sets grouped by C) OTV position in the probe and D) minimum restriction fragment length. Bottom panels show the number of probes in each bin for E) OTV position in the probe and F) minimum restriction fragment length.