Fig 2. Transition from collision at random angle to parallel alignment.

(A) Probability of reaching a parallel alignment as a function of the initial collision angle θ₀ and the number of continuous matched sites flanking the collision point N. Here q = 1/4. (B) Same as (A), for sequences where M sites flanking the collision point are the only ones not forced to match. (C) Fraction of attempted pairings that reach a parallel alignment as function of initial collision angle. Solid lines, mismatched random sequences with q = 1/16, 1/4, or 1/2, and with the E. coli genome statistics. Dashed line, perfectly matching sequences. (D) The results of (C) averaged over collision angles up to π/2, assuming collisions are uniformly distributed in 3d.