--force option in hybrid
I am using hybrid or hybrid-min with --force option.
What I would like to calculate is the free energy of 3'end-anchored hybridization (3'end 3base exact match).
Suppose the length of the input sequence is n, that can be calculated as
"hybrid --force (n-2),0,3 (sequence_1) (sequence_2)"
"hybrid --force 0,n,3 (sequence_2) (sequence_1)"
I was thinking those two give the same results.
However, the both commands produced different results.
So I would like to ask if my understanding is correct.
Thanks in advance.