Cleavage point determination by primer extension. The figure shows the electrophoresis gels for the primer extension reaction using the cleavage 3′ fragment RNA of each ribozyme as a template, and a ribozyme-specific reverse primer. A cytosine-sequencing reaction for each ribozyme is shown to provide a size marker (entire gels are shown in Additional file 1: Figure S4). The empty arrowheads indicate the maximum extension product corresponding to the cleavage point. The solid arrowheads indicate the helix P1 internal extension stop.