CPT can be used to detect specific DNA sequences and by extension specific genotypes. For example, CPT can be used to distinguish GMO produce from non-GMO produce. Clinically, CPT can be used as an alternative to cell culturing in order to detect antibacterial resistance of a pathogen.
CPT, at its core,  detects whether a specific sequence is present in a sample. But because cleaved probes accumulate following linear rate kinetics, the amount of target DNA can be quantified. Consequently, CPT has been used to quantify the number of non-coding repeats in organisms.
CPT can be used in conjunction with other technologies, like molecular beacons and qPCR.