Largo wrote:@Jarlve:
Thank you for the explanation!
Do you think that an intended change of transposition method instead of a mistake / misalignment?
Imagine Zodiac applied a transposition method not to the whole cipher at once. Instead he transposed the upper half and the lower half separately but with the same method. Let's say he had used a chunk based transposition with chunk size 6 and the key „5,3,4,2,1,6“. The upper half has 170 letters which leads to 28 complete chunks and 2 remaining letters which are not transposed. Same for the lower half. But in this case the pattern „5,3,4,2,1,6“ breaks in the middle of the cipher. Could this lead to a shift you described above? Maybe you could check this when applying your measurement only at distinct parts of the cipher (horizontally/vertically)? (But I am almost sure you did that already)
I don't know if it was intended and/or accidental.
The shift I am describing exists in a specifc scheme which we refer to as periodical transposition. In the next image I've shown the start of period 19. We call it period 19 because the distance between 1 and 2 is 19. If you measure bigrams in this way, especially at period 15 after mirroring or flipping the 340 there is a significant spike. Because of that it is very likely that such a periodical transposition exists in the 340. This managed to go undiscovered for some 45 years.

There are other transpositions which we have found that are very similar to a periodic transposition like this although it may be hard to understand why at first.
- Unkeyed columnar transposition (the period will be equal to the length of the columns)
- Diagonal transposition (the period will be equal to the length of the diagonals)
- Skytale (it is the same as in in the image though it wraps around the cipher instead of incrementing the position)
- Mr lowe's column shift (incrementally shift each column up or down, +1, +2, +3, etc)
- 2-dimensional period
- Column and row period
There can be additional rules, for example, what to do when your transposition revisits the same position.
In the Zodiac FBI files there exists a magic square 21 by 21. I discovered a possible link between it and the 340, they both generate period 19 bigram repeats. doranchak coded up this excellent tool
http://zodiackillerciphers.com/gridmaker/ which can generate periodic transposition tables like these.

There's also a possible link to Gareth Penn which at one point shows the exact same thing in his book Times 17.
