Note that by convention, the pair ((i,j) ) of neighbors of ego e is considered distinct from the pair ((i,j) ) of neighbors of (e').
For simplicity, we refer to pair i of SUs simply as SU i.
Call the set of edges modified the critical edges of the pair ((i,j)).
The multi loop is closed by a pair (i, j), where i < g.
Randomly select a base pair (i, j) (1 ≤ i < j ≤ N ).
Hairpin loops are uniquely determined by their closing pair (i, j).
Let r c i denote the rate of addition/deletion of domains of category c for genome pair i and let r i denote the overall rate of addition/deletion of domains for genome pair i.
e B (i, j, i ′, j ′) (E B (i, j, i ′, j ′), respectively) is the free energy (normalized energy, respectively) of the bulge or internal loop with exterior pair (i, j ) and interior pair (i', j' ).
e s (i, j ) (E S (i, j ), respectively) is the free energy (normalized energy, respectively) of the stack with exterior pair (i, j ) and interior pair (i + 1, j − 1).
