incorrect base pair indexing in pfme-scorer output

[ceheitsch]

Compare output in issue #6 with the correct thermodynamic decomposition for the o.nivara tRNA sequence (GGGGAUAUAGCUCAGUUGGUAGAGCUCCGCUCUUGCAAGGCGGAUGUCAGCGGUUCGAGUCCGCUUAUCUCCA) under the default Turner99 branching parameters (a = 3.4, b = 0, c = 0.4, d = 1) from mfold:

http://unafold.rna.albany.edu/results/11/20Oct21-11-41-47/20Oct21-11-41-47_1.full_det.html

Can be reconstructed from http://unafold.rna.albany.edu/?q=mfold/RNA-Folding-Form if needed.