Before revision:  Variations of data processing or modeling do not mitigate these errors. Instead, as evaluated by bootstrapping, the information content of SHAPE data appears insufficient to define these RNAs' structures.
After revision:  Variations of data processing , normalization, and modeling parameters did not significantly mitigate modeling errors. Only one varation, filtering out data collected with deoxyinosine triphosphate during primer extension, gave a modest improvement (FNR = 12\%, and FDR = 14\%). The residual structure modeling errors are explained by the insufficient information content of SHAPE data appears insufficient to define these RNAs' structures.