The Pairwise Alignment window displays all pairwise combinations of input sequences aligned with each other. Each pairwise alignment includes a summary report of the percentage, identity, percentage similarity, and number of gaps. For two sequences there is a single alignment, for three sequences there are three alignments, for four sequences there are six alignments, and so on. The alignments are derived from the complete multiple alignment, with all other sequences removed and all residual gaps closed. This approach closely matches the results of an independent pairwise sequence alignment.
Displaying multiple alignments
Multiple alignment text display