This is what I get using the nucleotide frequencies assumed by Deonier. The first block is for E. coli. The second is for M. genitalium.
The columns are: dinucleotide, observed count, expected count, Chi-square, c, Chi-square/c. Note that my values are close but not quite the same as in the book. Also there is (not shown) quite a bit of difference when the true nucleotide frequencies are used, even though they aren't very different than those assumed for this analysis. The values in the last column > 1 indicate a discrepancy between the value expected based on single nucleotide frequency and that observed in the sequence.
AA 86 62.5000 8.8360 1.3125 6.7322