Methods to identify dsRNA loci. (A) Clustered A-to-G changes in RNA-seq reads defined EERs, transcribed regions that form long dsRNA in vivo and are edited by ADARs. (B) Intronic duplex structures were predicted using UNAFold (Markham and Zuker 2008) to determine the folding free energy of intronic sequences of >40 and <9000 nt (example structure not to scale). To compare the stability of introns with different lengths, we normalized each intron's folding free energy to the number of nucleotides (ΔG/nt). (C) Inverted (green arrows) and tandem repeat (TR) (purple arrows) sequences were determined computationally from the C. elegans genome sequence using previously published tools (Materials and Methods) (Benson 1999; Warburton et al. 2004). Each defined repeat was ≥20 nt; arrows not to scale.
