Here are the first results of my tests of the effects of symbol merges on periodic ngrams. The motivation is: If there is a homophonic aspect to the cipher text, and the spikes in periodic ngrams are real indications of some transposition occurring in addition to substitution, then will we see higher ngram counts at interesting periods when we merge the correct symbols together?
I considered all possible combinations of pairs of symbols. For each pair of symbols:
1) Merge them in the Z340 cipher text (that is, replace all occurrences of the 2nd symbol with the 1st symbol)
2) Count the repeating ngrams in all periods from 1 to 170
3) Compare to repeating ngrams in all periods of the unmodified Z340. For example, if period 10 jumps from 20 bigrams to 25 bigrams when a symbol pair is merged, then the value I track is 25-20 = 5.
This generated a large amount of data so I made an interactive charting tool to help navigate it all:
http://zodiackillerciphers.com/symbol-merge-ngrams/Screenshot:

Click the image or link above to open the charting tool. The x-axis is the period, and the y-axis is the gain in repeating bigrams after merging the shown symbols. You can hover your mouse over the chart to see data values. Here is an explanation for the controls:
- Next: Show the chart for the next symbol pair
- Skip 20: Jump past the next 20 symbol pairs
- Last: Jump to the chart for the last symbol pair
- Prev: Show the chart for the previous symbol pair
- Skip 20: Jump past the previous 20 symbol pairs
- First: Jump to the chart for the first symbol pair
- Sort by: Here you can change how the charts are sorted:
1) Sum of increases in ngram repeats: This is the sum of ngram gains for all periods. Charts with the highest sums are shown first.
2) Max increase: Charts with highest gains in ngrams are shown first
3) Sigma: To compute sigma, we first compute mean and max gain for all periods, and standard deviation. Sigma is (max-mean) divided by standard deviation.
4) Period of max increase: Charts are arranged in order of which periods had the maximum gain in ngrams.
5) Period P spikes first (P can be from 1 to 170): Charts with max gain occuring at period P are shown first
6) Show data for: Here you can show charts for periodic 2-grams, 3-grams or 4-grams.
Let me know if there are any problems with the tool.
I find that it is very hard to judge the significance of the results, so I’m running a shuffle experiment and will update with those results soon. An early and interesting result is that merging


produces two 4-grams repeats at period 19 (because the merge produces one 5-gram repeat at period 19).


The shuffle experiment considers that to be significant since only 4% of shuffles for those merged symbols produced peaks of 1, and 96% of them were 0.