Sensitivity to mismatches as demonstrated by two-color hybridization. An array was synthesized containing reporters complementary to targets 5'-Cy3-GAC CTC CCG CTC ACG CAC CT (green) and 5'-Bodipy-GAC CTC CCG GAC ACG CAC CT (red), using standard conditions described in Materials and methods. The bases in bold are different in the two reporter:target molecules. The slide was hybridized with an equimolar mixture of the two labeled target oligonucleotides and the fluorescence intensity determined on the ScanArray 5000 using the Dapple spot-finding program. The green/red ratios of the green- and red-complementary features were 3.12 ± 0.57 (N = 230) and 0.25 ± 0.05 (N = 660), respectively. Graphing Cy3 intensity vs Bodipy intensity shows excellent separation between signals and the insert shows that the effects of two base changes are clearly distinguishable by eye.