. 2017 Jun 21;45(14):e136. doi: 10.1093/nar/gkx538

Table 1. The relationship between (r_i, r_j) and (t_i, t_j) for the base-pairing annotation inferability.

Relationship	Description
Common base pairs	(r_i, r_j) ∈ S_R and (t_i, t_j) ∈ S_T, and both
	have the same type of interacting edges and
	cis/trans orientation
Unrelated	Neither of (r_i, r_j) or (t_i, t_j) is annotated
	as a base pair
Non-inferable—case 1	(r_i, r_j)∈S_R, but one or both of t_i and t_j is ‘—’
Non-inferable—case 2	(t_i, t_j)∈S_T, but one or both of r_i and r_j is ‘—’
Inferable—case 1	(r_i, r_j)∈S_R, and t_i, t_j are bases (not gap)
Inferable—case 2	(t_i, t_j)∈S_T, and pair of bases (r_i, r_j) ∉ S_R

Table 1. The relationship between (ri, rj) and (ti, tj) for the base-pairing annotation inferability.