Is there a way to select 2 paired nucleotides and swap their types?
Yes, the little symbol to the far right of the 4 colored circles on the bottom. It looks like two circles with triangles between them.
If you hover over it, it says “Swap Paired Bases”. The Hotkey for it is 5.
Select that and click on the paired base to swap them. (Unless they have a key in one, and then they are locked that way…)
You can also click on the arrows between two colors and it will select the base pair. If your taking a base pair (blue and yellow) and clicking on a base that already has the same colors. It will swap them as well.