Drop-Phase schematic.

<p>A genomic DNA sample is emulsified into aqueous droplets in an oil-aqueous reverse emulsion. Allele-specific fluorescence probes (FAM, blue; and HEX, green) are used to detect alleles at two different loci. Following PCR, the droplets are positive for one fluorophore (blue or green), positive for both fluorophores (orange), or positive for neither fluorophore, depending on the alleles they contained at the beginning of the reaction. (<b>a</b>) <i>Trans</i>-configured alleles partition independently into droplets. Co-partitioning (orange) is therefore governed by chance. (<b>b</b>) <i>Cis</i>-configured alleles tend to co-segregate into the same droplets, because they are physically linked; co-partitioning greatly exceeds chance expectation. (<b>c</b>) Restriction digest at a site between the <i>cis</i>-configured alleles abolished co-partitioning of the two alleles; co-partitioning again occurs to the extent expected by chance.