Figure 19

An alignment with folding of type II. In such an alignment with folding the first and last alignment columns are not paired to each other, i.e. the last column is either paired to some other column (as in (a), which consists of columns 1 to 15 of the alignment with folding presented in Figure 17b), or it is unpaired (as in (b), which consists of columns 1 to 5 of the alignment with folding presented in Figure 17b). In both cases, the alignment with folding may be decomposed into two alignments with foldings (A', F') and (A", F"), where (A', F') is an alignment with folding for S_{X, Q}and (A", F") is an alignment with folding for S_{Q, Y}, for some Q ∈ (X, Y).