The ability to use ctrl-click to mark/unmark a base and the switching between natural/target mode is very useful in chasing down pairing problems.
If we could use a click on the pairing probability dot-plot to mark (and/or unmark) the bases that correspond to the X-Y coordinates that could make finding and eliminating the *lower probability* miss-matches easier as well.
Alternatively (or additionally), hovering over an X-Y point on the minimized dot-plot could temporarily highlight the two implied bases. This would not be as precise as on the large plot as it is hard to read and position within the smaller dot plot.
In the same vain, optionally using a binned heat-map color-scale (say 4-7 bins) might make reading the dot-plot easier (for those who are not color-blind, that’s why it needs to be optional).