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Variation in reactivities reconstructed by the scheme in Ding et al. (2014) and computed from 100,000 RPE simulations of 77.5 × 103 reads. Box boundaries mark tenth and ninetieth percentiles of the empirical distribution; plus signs mark target normalized SHAPE reactivities in the fictive 775 nt-long RNA depicted in Figure 5. Hit and primer rates are 0.003 per site, and shown is a middle window of reactivities to circumvent end-effects.
