Figure 4.

Reproducibility of FAST. (A) Two separate SHAPE experiments analyzed by FAST, in which the same primer was used during RT. The resultant SHAPE reactivities are plotted against one another and demonstrate the strong reproducibility of the FAST method to accurately assign NT position, correct for signal decay, and adjust for loading differences. See also Figure 1. (B) Two separate SHAPE experiments, in which two different but nearby primers were used during RT. The resultant SHAPE reactivities are plotted against one another. The observed correlation suggests against the possibility that the peak identification algorithm is specific to one primer, and that instead, it is a general means of correlating peaks with NT positions.