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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010298836,0.015411731,0.012605324,0.099461441,0.000000000],[0.183597737,0.020032766,0.114256328,0.014605825,0.000000000],[0.012787512,0.111208410,0.002738939,0.018310925,0.000000000],[0.127973890,0.013816041,0.231031993,0.011862304,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [10] // Basepair U858 - G919 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [2] | Right Index [9] | Norm Constant [0.111475469623490] // Cluster node 9DFE|1|1A|G|859:9DFE|1|1A|U|860 and 9DFE|1|1A|A|917:9DFE|1|1A|A|918
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018239161,0.004036356,0.018944354,0.004036356,0.000000000],[0.040590873,0.325253122,0.004036356,0.004036356,0.000000000],[0.004036356,0.009675411,0.030696143,0.017952320,0.000000000],[0.451254601,0.004036356,0.023418451,0.039757431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|860 - 9DFE|1|1A|A|917 tWH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.062361437,0.057705919,0.002268717,0.155865386,0.000000000],[0.059749066,0.057747365,0.002268717,0.002268717,0.000000000],[0.227779157,0.002268717,0.182026226,0.060678325,0.000000000],[0.063644679,0.058830138,0.002268717,0.002268717,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|859 - 9DFE|1|1A|A|918 tSH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.028328682,0.028865628,0.001587122,0.028209980,0.000000000],[0.021149212,0.031872234,0.000351416,0.028269118,0.000000000],[0.173255801,0.002459910,0.211342544,0.353133826,0.000000000],[0.028768228,0.028595529,0.000351416,0.033459355,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|859 - 9DFE|1|1A|U|860 cSH 
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 [4] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.153505275,0.132858197,0.164722656,0.135255665,0.000000000],[0.077590391,0.096711001,0.001476291,0.130802101,0.000000000],[0.001476291,0.001476291,0.009828022,0.001476291,0.000000000],[0.007909813,0.001476291,0.081959135,0.001476291,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [4] | Right Index [7] // Basepair A861 - G916 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010506046,0.072905153,0.011167534,0.171916865,0.000000000],[0.016914358,0.009958243,0.163684434,0.012687218,0.000000000],[0.011039949,0.196202645,0.002245259,0.092635778,0.000000000],[0.172186808,0.013108791,0.026826027,0.016014892,0.000000000],[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 [5] | Right Index [6] // Basepair G862 - C915 cWW 
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
