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 [9] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000319870323534092682713332759317165949125] | Num Left Bases [5] | Num Right Bases [4] | Left Index [1] | Right Index [9] | Norm Constant [0.004461019866877] // Cluster node 4WF9|1|X|G|909:4WF9|1|X|U|913 and 4WF9|1|X|A|954:4WF9|1|X|C|957
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.029558166,0.003453297,0.098788114,0.003453297,0.000000000],[0.401933476,0.025159497,0.003453297,0.003453297,0.000000000],[0.003453297,0.012056445,0.031053956,0.031831792,0.000000000],[0.034727452,0.003453297,0.015526095,0.298645225,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|910 - 4WF9|1|X|A|954 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.008693416,0.016882694,0.009536121,0.188912817,0.000000000],[0.021212105,0.009460668,0.189548413,0.010628111,0.000000000],[0.009554720,0.187122556,0.001967108,0.022177826,0.000000000],[0.253314615,0.009983070,0.051283436,0.009722321,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|U|913 - 4WF9|1|X|A|954 cWW 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.003679589,0.053642867,0.004190070,0.076104487,0.000000000],[0.006463298,0.025257446,0.076749356,0.005021698,0.000000000],[0.004143537,0.609465400,0.000789802,0.010117932,0.000000000],[0.075130495,0.036484266,0.008868823,0.003890933,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|909 - 4WF9|1|X|C|957 cWW 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.029105501,0.246113907,0.028691084,0.029298906,0.000000000],[0.057189470,0.460197441,0.000859964,0.058134750,0.000000000],[0.007437840,0.006019749,0.013027246,0.003560805,0.000000000],[0.004581468,0.047962116,0.003577953,0.004241800,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|912 - 4WF9|1|X|C|957 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.144299127,0.143607793,0.001793530,0.008672475,0.000000000],[0.167834763,0.007908239,0.001793530,0.007170510,0.000000000],[0.321720112,0.001793530,0.001793530,0.005881590,0.000000000],[0.155211804,0.007794610,0.014112197,0.008612658,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|909 - 4WF9|1|X|A|911 tSW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.074081710,0.074659521,0.004122880,0.073037140,0.000000000],[0.138620443,0.123994722,0.000862589,0.060014733,0.000000000],[0.063494280,0.000862589,0.075730924,0.078233932,0.000000000],[0.075870334,0.075861931,0.000862589,0.079689684,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|910 - 4WF9|1|X|C|912 cSH 
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4WF9|1|X|A|955
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4WF9|1|X|A|956
Insertion    | Location [2] | Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | 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
