Hi Moritz,
It is based on phylogenetic tree, the substitution
comparison from lower nodes must be compared to higher level.
E.g. For column 11, the bases for row 3 is compared to row 1.
Same result will also be given if we compare row 3 to row 2.
Both row 1 and row 2 has higher level than row 3 row 4 in
phylogenetic tree.