Although it might be counter-intuitive, note that a site where two nucleotides are identical and the other two nucleotides are different (site 2 in the figure above) is NOT a topology-defining site. An explanation is given in the figure below.
The top row shows different topologies that explain the nucleotide configuration equally well (in terms of the required number of nucleotide substitutions). Consequently, this nucleotide configuration is NOT a topology-defining site.
In the bottom row, one topology is distinguished in that it can be explained by a smaller number of nucleotide substitutions than the other topologies. Consequently, this nucleotide configuration is a topology-defining site.
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