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 [0.0000239574126029] | Pair Probability [[0.004641539,0.008323395,0.026680104,0.096752579,0.000000000],[0.009868707,0.004727273,0.547012770,0.006712030,0.000000000],[0.005395946,0.098837337,0.005085512,0.011421215,0.000000000],[0.098006880,0.006466912,0.065149048,0.004918754,0.000000000],[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 [12] // Basepair C1311 - G1659 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.411121066118020] // Cluster node 7A0S|1|X|G|1312:7A0S|1|X|A|1314 and 7A0S|1|X|A|1658:7A0S|1|X|A|1658
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.042857649,0.045370598,0.000514478,0.002424734,0.000000000],[0.043176051,0.045265538,0.000514478,0.000514478,0.000000000],[0.398595795,0.003601343,0.017605820,0.305668340,0.000000000],[0.047840582,0.045021164,0.000514478,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|1312 - 7A0S|1|X|A|1658 tSH 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.372030251,0.029374515,0.003431841,0.015507529,0.000000000],[0.003431841,0.014563521,0.008501137,0.003431841,0.000000000],[0.302750037,0.003431841,0.126145626,0.016448812,0.000000000],[0.044064595,0.003431841,0.036733349,0.016721423,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|A|1314 - 7A0S|1|X|A|1658 tHW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|U|1313
InitialNode  | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.583333333,0.083333333,0.083333333,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Initial node 7A0S|1|X|G|1316 - 7A0S|1|X|A|1657 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.704545455,0.250000000,0.022727273,0.022727273,0.000000000] | Position [2] | Left Index [5] | Right Index [10] // Fixed node on right for 7A0S|1|X|U|1656
InitialNode  | Left Length Distribution [1.000000000] | 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 [5] | Right Index [9] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [5] | Right Index [9] // Junction node G1316 - U1656 ID J6787
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G1316 - C1641 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] | Right Index [9] // Initial node 7A0S|1|X|G|1642 - 7A0S|1|X|U|1656 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 7A0S|1|X|C|1641
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 [0.0000224863733088] | Pair Probability [[0.010822634,0.088558519,0.011090157,0.189427059,0.000000000],[0.016147531,0.010174201,0.153929377,0.011868934,0.000000000],[0.010975303,0.167484236,0.002308725,0.121823196,0.000000000],[0.153826251,0.012646641,0.020567725,0.018349512,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // Basepair A1643 - U1656 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
