To ensure that this phenomenon was not an artifact of the processing pipeline the effect was replicated with a three-state toy model (example 1 in Trendelkamp et al. ). 10 000×20step trajectories were sampled from the same 3 × 3 transition matrix and for each trajectory count matrices (C 00/0t/tt ) were calculated. We assert that the differences in the count matrices arising from the finite sampling in this toy model are similar to the differences from different discretization schemes in the example of BBA. From each set of count matrices t 2 and VAMP2(2) scores were estimated and these are shown in Figure panel (a). While t 2 is clearly rank-correlated with VAMP2(2), the rank correlation is not perfect. Many subsets of these results form sets which are anti-correlated, three examples of this inverse relationship are shown as black lines labeled 'Inverse'. These subsets mirror the effect seen in the BBA models in Figure . As a comparison, in panel (b) we plot the sum of the squares of the first two eigenvalues, VAMP2 eq (2), which shows perfect rank correlation (as they must).