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