Figure 3

Illustration of induced base pairing proclivities formulated in (1). Heavy lines represent the sequences with nucleotide positions indicated by thick dashes. The dashed lines between k and l, and between i and j represent potential base pairing interactions. The probability of base pairing between k and l is shown as _p π^s(k, l). The dashed arrows indicate the co-incidence of k with i and l with j. The base pairing probability of nucleotides at k and l in x _s induces base pairing proclivities for nucleotides at i and j in x _m based on alignment co-incidence probabilities _c π^(m,s)(i, k) and _c π^(m,s)(j, l) resulting in an induced proclivity .