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Table 1 Parameters used to evaluate hairpins

From: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

Pairing Energy
G-C -2.3
A-T -0.9
G-T 1.3
Mismatch 3.5
Gap 6.0
Loop_pen(n) 1ยท(n - 2)
  1. Parameters used to evaluate the energy of a potential hairpin where n is the length of the hairpin loop.