Table 1

Parameters used to evaluate hairpins

Pairing
Energy

G-C
-2.3
A-T
-0.9
G-T
1.3
Mismatch
3.5
Gap
6.0
Loop_pen(n)
1·(n - 2)

Parameters used to evaluate the energy of a potential hairpin where n is the length of the hairpin loop.

Kingsford et al. Genome Biology 2007 8:R22   doi:10.1186/gb-2007-8-2-r22