Figure 1.

An alignment of the target sequence with an intermediate and a putative homolog. The dotted and the dashed lines represent the intermediate aligned to the putative homolog and the target, respectively. The positions of the starting residues in the alignment of the intermediate with the putative homolog and the target are denoted by i^t_s and i^q_s, respectively. The positions of the ending residues are denoted by i^t_e and i^q_e. The number of residues in the common overlap region of the intermediate is indicated by C.