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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008957994,0.017378845,0.010148388,0.188059271,0.000000000],[0.018441409,0.009141765,0.220204749,0.012196759,0.000000000],[0.010152962,0.219609041,0.001962745,0.023232061,0.000000000],[0.208491401,0.012038445,0.030373981,0.009610184,0.000000000],[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 [12] // Basepair G15 - C8 cWW 
ClusterNode  | Deletion Probability [0.0000000000015373] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.419423571192567] // Cluster node 3NVI|1|F|C|16:3NVI|1|F|G|19 and 3NVI|1|F|A|7:3NVI|1|F|A|7
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.211158828,0.039489841,0.039905912,0.038865149,0.000000000],[0.155364558,0.022023296,0.023744397,0.022023296,0.000000000],[0.170324966,0.022023296,0.023421606,0.036949968,0.000000000],[0.128634998,0.022023296,0.022023296,0.022023296,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NVI|1|F|C|16 - 3NVI|1|F|A|7 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.051125900,0.054123656,0.000613732,0.002892522,0.000000000],[0.051505729,0.053998327,0.000613732,0.000613732,0.000000000],[0.393981458,0.003068662,0.015001713,0.260456406,0.000000000],[0.057070158,0.053706807,0.000613732,0.000613732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NVI|1|F|G|19 - 3NVI|1|F|A|7 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.150000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.050000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.550000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3NVI|1|F|G|17
Insertion    | Location [1] | Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
Insertion    | Location [2] | Length Distribution [0.128145746,0.742627760,0.128184345,0.001003551,0.000038598] | Letter Distribution [0.050000000,0.050000000,0.050000000,0.850000000,0.000000000]// Insertion after nucleotide 3, 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 [5] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.051125900,0.051505729,0.393981458,0.057070158,0.000000000],[0.054123656,0.053998327,0.003068662,0.053706807,0.000000000],[0.000613732,0.000613732,0.015001713,0.000613732,0.000000000],[0.002892522,0.000613732,0.260456406,0.000613732,0.000000000],[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 [5] | Right Index [10] // Basepair A20 - G6 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014100605,0.258622283,0.036783010,0.021988284,0.000000000],[0.015584515,0.040997510,0.018794731,0.013820321,0.000000000],[0.012326511,0.019146131,0.003886384,0.049649293,0.000000000],[0.019208232,0.014967397,0.015930823,0.444193970,0.000000000],[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 [6] | Right Index [9] // Basepair U21 - U5 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009860579,0.052006811,0.010711944,0.185943858,0.000000000],[0.015798891,0.009401807,0.171033885,0.012333004,0.000000000],[0.010586262,0.231672514,0.002103895,0.072801947,0.000000000],[0.168237118,0.012925649,0.021034647,0.013547190,0.000000000],[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 [7] | Right Index [8] // Basepair G22 - C4 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
