Figure 1.
Some ways of extending an alignment in both directions from a small “core” alignment (black). In each direction, an optimum alignment extension is sought from among all possible ones within the gray area. (A) Simple toy method: The gray areas are blocks of predefined size n × n. (B) Realistic example: The gray areas are adjusted as the calculation proceeds, attempting to follow good alignments. (C) Unlimited extension from zero-size core.
