Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node U27 - A11 from junction 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [6] | Norm Constant [0.254951209121093] // Cluster node U27:U27 and A10:A11
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009469891,0.020059356,0.010603791,0.196533016,0.000000000],[0.020450148,0.008797341,0.197253072,0.011592952,0.000000000],[0.010539143,0.219155954,0.002110264,0.025117588,0.000000000],[0.219177973,0.011880534,0.025324236,0.011934740,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U27 - A11 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.137818189,0.103088651,0.005213033,0.004518119,0.000000000],[0.106359205,0.100311682,0.001185874,0.104577052,0.000000000],[0.005542935,0.005354284,0.005993321,0.099240131,0.000000000],[0.010111954,0.209208468,0.001185874,0.100291229,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A10 - A11 cSH 
InitialNode  | Left Length Distribution [0.490496628,0.012262416,0.490803188,0.006131208,0.000306560] | Left Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Initial node G28 - U9 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Position [2] | Left Index [2] | Right Index [4] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009999033,0.020370037,0.011577394,0.189754219,0.000000000],[0.016871198,0.008244913,0.204374808,0.013008374,0.000000000],[0.011431659,0.249278495,0.002108170,0.027040831,0.000000000],[0.188658474,0.013655008,0.023325621,0.010301767,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // Basepair G28 - C8 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
