Figure 1.

A parse tree for the grammar of Table 1. Each internal node is labeled with a nonterminal (Stem or Loop); additionally, the subsequences (X_ij, Y_kl) generated by each internal node are shown. The parse tree determines both the structure and alignment of the two sequences. The cut-points of the alignment are the sequence co-ordinates at which the alignment can be split, i.e. {(0, 0), (1, 1), (2, 2) ... (15, 12), (16, 13), (17, 14)}.