All real-time PCR methods in the Auburn University Molecular Diagnostics Laboratory detect targets by measuring light emitted by fluorescent probes.

Real-time PCR design for amplification of the DNA coding for the 18S rRNA of protozoal parasites.  The alignment of homologous parasite sequences shows conserved and divergent sequence regions.  Primers are shown as lines with arrows (Hepatozoon americanum or H. canis: light blue; Babesia gibsoni or B. canis: dark blue).  Probes are shown as black lines, with the green triangle indicating the green fluorescent energy donor dye, and the red triangle indicating the energy acceptor dye that emits red fluorescence after stimulation of the donor dye by blue light.  Specificity of the primers and probes is ensured by targeting sequence regions that differ between the parasites.

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