I have pushed a new version of Examine that will let you lock letters like ZKDecrypto, see the last post in: viewtopic.php?f=81&t=2432 If you or anyone has any questions about it just shoot.
@doranchak,
I personally don't give much value to how many repeats a piece of a cipher has. While I do find it of importance when considering forced, manual solutions that degrade quickly. The solver looks at the entire cipher. For example, in the following image I selected the first 8 symbols of the 340 and you can see how they "connect". I believe this is the real structure, roughly, the amount of symbols involved with a change. Maybe I misunderstood your point, I'll think about it for a while.

@glurk,
The negative score is interesting, I wonder if it might help with ciphers which solution is lower than the local maxima. I once tried to penalize for less flat n-gram scores but it didn't help. What do you think about an IoC for consonant/vowel frequencies? For instance, a double consonant on average appears 50 times in a 340 character cipher, a triple 11 times etc, etc... (made up values).

