An important aspect of rapid cycling is cleaner product. Rapid cycling leaves less time for primer extension at non-specific annealing sites. The amount of nonspecific product is directly related to the time spent at low temperatures 1 Wittwer, CT, Garling, DJ 1991.
Faster cycling produces cleaner electrophoresis gels.
Cycle sequencing reactions done in the RapidCycler are cleaner and more readable than parallel reactions done in a conventional heat block cycler 2 Swerdlow, H.K. Dew-Jager, and R.F. Gesteland. 1993. Rapid Cycle Sequencing in an Air Thermal Cycler. If low specificity is desired, the RapidCycler can be programmed for hold times. If you want maximum specificity, the RapidCycler is the only choice. Samples were cycled 30 times through profiles A, B, C, and 10 l of the product were electrophoresed and viewed by ethidium bromide staining.