I was would like to have a new tool one that would highlight 3 or more repeated sequences. Or you could set to see 3,4,5 or any number of repeated sequences.
could help keep stop bad pairings
Joshua:
This is a great suggestion! Actually, one of the player strategies looks for repeated sequences, and I think it’s doing rather well in our tests (perhaps someone else can comment).
Your suggestion has been added as feature #522 in the EteRNA bug tracker. You can track it there.
As you know, our big push right now is getting experimental results ready for our first publication, so we may not get to this immediately, but I think that the idea of visualizing the best player strategies definitely is interesting!
I would be happy at this point in my gaming to have the tool which would highlight the repeated nucleotides that are disallowed in a given puzzle, which might be a subset of this tool. It is frustrating to have to go back and find the too-long run in a puzzle. Or at least maybe if when you violated this condition there was a sound in the game.
oolong -
Thank you for your great idea!
I added it our tracker as feature #530.
We will bring up this topic in our next meeting.
Hi Adrien
There are more then one player that has looks for repeated sequences in their strategy
Mat
Mat: That’s a great point, and we know! Ultimately, an importnat step will be to fold the best and most useful player strategies directly into the UI, but we’re working constantly already and everything takes time and money. We’re working on the latter, and if you have any ideas to make more of the former, please let us know! 
Just found out from Adrien that CTRL click (or command click on a mac) highlights a base
that means you can mark some bases, in target mode, switch to natural mode, mark some more bases (that those bases paired with) switch back to target mode
and then you should have found another matching set of bases
Hi Joshua
This feature has been implemented in the latest update.
Thanks for sharing your idea!