Figure 2.

Not all alignable character pairs can be detected by global alignment. In the shown example, two homologous sequences seqA and seqB are separated by one TR unit duplication and two subsequent deletions. Each character in the TR region of seqA retains a corresponding homologous character in seqB, but the global alignment is unable to detect all such relationships owing to the requirement of retaining the character order of each sequence (character A in seqA is not aligned to the homologous A in seqB). Although such alignment does not fully reflect the homology in terms of aligned pairs, it nevertheless correctly reflects the three indels.