# Add -2.0 kcal/mol per unpaired nucleotide at positions 10-20
E 10 0 10 -2.0

# Do not allow multibranch loops
P 1 0 100 Mm

# Force the first 3 nucleotides to be paired
F 1 0 3

# Ligand motif 'AAA' in all loop types
UD  AAA   -5.0    A

# Ligand motif 'CCC' in exterior loops
UD  CCC   -3.0    E
