Comparison of sequences. a) Alignment of 5 poxvirus DNA polymerase proteins. In this example, the blue boxes, shown under a sequence, indicate a difference to the top sequence in the MSA. b) Similarity plot calculated with a PAM250 matrix of the MSA shown in (a). The Reference Sequence, Window Sizeand Step Sizecan be changed, and the user can zoom into a particular region by using the cursor to draw box on the plot; Re-centrereturns the plot to the full size.