Jump rate is understood as the probability per unit time for a transition between two sites. When considering an n-site jump one can have in general n(n-1) different jump rates. However, you have to supply one rate only, together with a selection of that transition, for which this rate should hold. In case of a 2-site jump you may choose between the transition from 2 to 1 (1 ← 2), which is the default, and the opposite. The specification of the transition is important, if you have different populations.

In the case of 3,4 or 6 sites one has 6, 12 or 30 different transitions, which can be entererd by means of a transition matrix, which contains the rates relative the one selected.