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Relative standard deviations (RSD) of ML reactivity estimates computed from 100,000 SHAPE-Seq simulations at a range of hit rates. (A) Target normalized SHAPE reactivity profile of the P546 domain of the bI3 group I intron, following omission of negligible reactivities. RSD per nucleotide values are grouped for hit rates 3 and 2 (B), 2 and 1 (C), and 0.5 and 0.1 (D). Vertical scale for the low-rate plot is >5 times the scale for high-rate plots.
