Figure 2

An example of relations of indices of stem components in SCS alignment. α _i /β _j and p _i /q _j in equation (1) are the indices (smaller than i/j) of stem components of X/Y. The red lines separate the stem components into groups which have the same positions in RNA sequences. When X _i and Y _j match in DP of SCS alignment, the stem components of the adjacent previous match must be either non-overlapping or 1-continuous with X _i /Y _j . $X_{{\alpha }_i}/Y_{{\beta }_j}$ are 1-continuous with X _i /Y _j . $X_{p_i}/Y_{q_j}$ are the nearest stem components that do not overlap with X _i /Y _j .