Holding the shift key and dragging the left mouse down highlights a number of bases. Holding shift key and tapping the left or right arrow key would shift the string of highlighted bases. Shifting no longer moves the bases.
Holding the shift key and left clicking the mouse away from the bases but in the state 1 frame used to make the highlighted bases go away. It no longer clears the highlighted bases.
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The first issue you describe is specific to pip mode (if you go to single-state view mode, shifting should work as expected), and has been noted. The latter issue is new though. I noticed that if you click “within” the RNA strand (ie, where the base numbers are) it will unhighlight the bases. I’ll look into fixing the fact that clicking outside fails to do so though!
Thanks, if I creep up to the edge of the gray line from outside the RNA strand, I can make it disappear. Also works by clicking in a loop inside the strand.