Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [1] | Right Index [8] // Basepair G10 - C29 cWW 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [4] | Num Right Bases [2] | Left Index [2] | Right Index [7] | Norm Constant [0.007328414636428] // Cluster node 5U3G|1|B|G|11:5U3G|1|B|C|14 and 5U3G|1|B|G|27:5U3G|1|B|U|28
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|C|14 - 5U3G|1|B|G|27 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.045965469,0.300684085,0.003676754,0.003676754,0.000000000],[0.023538170,0.014096579,0.003676754,0.003676754,0.000000000],[0.003676754,0.003676754,0.172811225,0.406136932,0.000000000],[0.003676754,0.003676754,0.003676754,0.003676754,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|G|11 - 5U3G|1|B|U|28 bif 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.015131034,0.277521604,0.013509461,0.023595120,0.000000000],[0.016723384,0.018031943,0.020168192,0.014830267,0.000000000],[0.013227295,0.020545271,0.004170389,0.053277511,0.000000000],[0.020611910,0.016061168,0.017094999,0.455500452,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|U|13 - 5U3G|1|B|U|28 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.075162086,0.075504064,0.004224789,0.076442643,0.000000000],[0.074797160,0.086127893,0.000932278,0.077317705,0.000000000],[0.076126663,0.000932278,0.078408891,0.088765037,0.000000000],[0.076691089,0.075945794,0.000932278,0.131689351,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|U|12 - 5U3G|1|B|U|13 cSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.088942412,0.095317025,0.008286587,0.090773273,0.000000000],[0.090993081,0.093096767,0.001058558,0.011953521,0.000000000],[0.013374065,0.001058558,0.096560837,0.086137347,0.000000000],[0.090839268,0.144317297,0.001058558,0.086232846,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|U|12 - 5U3G|1|B|C|14 cSH 
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
