Complete example using a tiny, contrived RNA. (A) Alignment of fictional RNAs, in Stockholm format . The "#=GC SS_cons" line specifies a stem (shaded blue rectangles) based on matching angle brackets (< and >). The "#=GC R2R_LABEL" line associates the labels [, ], 1, 2 and T with specific columns. The labels are used in R2R markup (e.g., see text "label & use"). (B) Raw output of R2R when run on the input in part A.