First, it took me awhile to notice that I could expand the display showing the “stability” of the chain so that I could see it better. However, it auto reduces back to it’s normal size, meaning that I’m constantly clicking between it and the main display.
I’d suggest that the “stability” drawing be done to scale under the chain, thus giving the effect of the chain “outlined” in red or white. This could be optional and it could be awarded as an additional tool for an early achievement.
An alternative would be to simply change the outline of the base pairs that are not stable or to us the same “box” highlight that is used to indicate longer than allowed sequences.
(I know, you should never allow another programmer to play with your software as they will want things done the way they want, or just be generally annoying 
)