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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003750350,0.054674460,0.004270648,0.077568035,0.000000000],[0.006587592,0.025743166,0.078225305,0.005118269,0.000000000],[0.004223220,0.601955120,0.000804991,0.010312508,0.000000000],[0.076575313,0.037185886,0.009039378,0.003965758,0.000000000],[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 [14] // Basepair G1111 - C1134 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.110577593,0.117061285,0.001327410,0.006256089,0.000000000],[0.111399105,0.116790218,0.001327410,0.001327410,0.000000000],[0.171202567,0.001327410,0.006489287,0.112665566,0.000000000],[0.123434124,0.116159705,0.001327410,0.001327410,0.000000000],[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 [2] | Right Index [13] // Basepair G1112 - A1133 tSH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.442799386,0.324831327,0.019385716,0.019778053,0.000000000],[0.050816783,0.000577625,0.049242991,0.005488648,0.000000000],[0.002879881,0.048613671,0.001441753,0.000577625,0.000000000],[0.003923273,0.028488016,0.000577625,0.000577625,0.000000000],[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 [3] | Right Index [12] // Basepair A1113 - A1132 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [11] | Norm Constant [0.269832767432214] // Cluster node 8P9A|1|sR|G|1114:8P9A|1|sR|U|1115 and 8P9A|1|sR|A|1131:8P9A|1|sR|A|1131
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018414538,0.004075167,0.019126511,0.004075167,0.000000000],[0.040981170,0.328380556,0.004075167,0.004075167,0.000000000],[0.004075167,0.009768444,0.030991298,0.018124938,0.000000000],[0.445978203,0.004075167,0.023643628,0.040139714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|U|1115 - 8P9A|1|sR|A|1131 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.030507812,0.031086061,0.001709208,0.030379978,0.000000000],[0.022776075,0.034323944,0.000378448,0.030443666,0.000000000],[0.186583170,0.002649134,0.227599663,0.303374889,0.000000000],[0.030981169,0.030795185,0.000378448,0.036033152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|G|1114 - 8P9A|1|sR|U|1115 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 [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.174590976,0.050781800,0.314754513,0.052967675,0.000000000],[0.049529943,0.041486312,0.002890767,0.050817093,0.000000000],[0.001714182,0.000575619,0.014852767,0.000575619,0.000000000],[0.009918595,0.000575619,0.233392901,0.000575619,0.000000000],[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 [6] | Right Index [10] // Basepair A1116 - G1130 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 8P9A|1|sR|U|1117
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015535214,0.291177596,0.014042294,0.082956205,0.000000000],[0.013458861,0.012543449,0.035731204,0.014127935,0.000000000],[0.013741462,0.040763683,0.003181999,0.356661451,0.000000000],[0.035874902,0.015432038,0.014121064,0.040650641,0.000000000],[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 [8] | Right Index [9] // Basepair G1118 - U1129 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
