  In this paper, we study the interaction of an antisense RNA and its target
mRNA, based on the model introduced by Alkan {\it et al.} (Alkan {\it et al.},
J. Comput. Biol., Vol:267--282, 2006). Our main results are the derivation of
the partition function
  \cite{Backhofen} (Chitsaz {\it et al.}, Bioinformatics, to appear, 2009),
based on the concept of tight-structure and the computation of the base pairing
probabilities. This paper contains the folding algorithm {\sf rip} which
computes the partition function as well as the base pairing probabilities in
$O(N^4M^2)+O(N^2M^4)$ time and $O(N^2M^2)$ space, where $N,M$ denote the
lengths of the interacting sequences.
