6.8 years ago by
Davis, California, USA
No matter what the length of A and B are, A' and B' (the aligned sequences) will be of the same length. This simply comes from the definition of an alignment. The characters (representing base pairs) from the two sequences are arranged as to minimize the differences between them, and then the empty spaces (if any) are filled in with gaps (dash characters). These gaps are typically interpreted as evolutionary events between two homologous sequences, i.e. an insertion of nucleotides to one sequence or a deletion of nucleotides from the other (indels).