For the Discussion?

We need to remember that the uptake bias specified by the position-weight matrix the model uses isn't the effective bias in the run. Instead, the effective bias changes within each cycle and between cycles. In each cycle it typically starts with even the perfect-US fragments having only a 10% chance of recombining, and decreases gradually to a point where the disparity between perfect and less-than-perfect US is substantially reduced. How substantially depends on how many US the genome has at that cycle.