Most 18S structural features are accessible to probe targeting. The target sites of tested probes in the Drosophila 18S rRNA are shown. The secondary structure representation is based on data from the 3D structure and constructed using the RiboVision program (Anger et al. 2013; Bernier et al. 2014). Some probe target sites are overlapping because we designed a second set of high Tm probes against the 5′ side of the 18S (probes #21–30, see Fig. 1). To distinguish between the individual target sites, we have alternated the colors between red and blue, with the overlapping portions of probe target sites shown in yellow. The labels for the target sites of probe #2 and #29 are highlighted in red.
