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
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [10] | Norm Constant [0.256806238322926] // Cluster node 4V9F|1|9|U|33:4V9F|1|9|C|36 and 4V9F|1|9|A|47:4V9F|1|9|A|47
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.008557538,0.018275361,0.009275439,0.223652173,0.000000000],[0.018746003,0.009095718,0.183160424,0.010050260,0.000000000],[0.009277461,0.182896714,0.001911679,0.034113629,0.000000000],[0.233674193,0.009980139,0.037277643,0.010055624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|33 - 4V9F|1|9|A|47 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.016615310,0.020502196,0.014739411,0.020124104,0.000000000],[0.283439392,0.229531818,0.002418326,0.282844622,0.000000000],[0.025252980,0.002418326,0.026136650,0.010123545,0.000000000],[0.015802802,0.024193865,0.011325751,0.014530901,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|36 - 4V9F|1|9|A|47 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.136363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.318181818,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|A|34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.045454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.863636364,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|C|35
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 [9] // Initial node 4V9F|1|9|C|37 - 4V9F|1|9|C|46 from node 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [1] | Num Right Bases [4] | Left Index [5] | Right Index [9] | Norm Constant [0.530365125233084] // Cluster node 4V9F|1|9|C|37:4V9F|1|9|C|37 and 4V9F|1|9|G|43:4V9F|1|9|C|46
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.003503974,0.006283467,0.004028249,0.073040105,0.000000000],[0.052150337,0.024980872,0.620047911,0.035469147,0.000000000],[0.004073488,0.074613923,0.000767827,0.008622062,0.000000000],[0.073986997,0.004881977,0.009836416,0.003713248,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|37 - 4V9F|1|9|G|43 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.006847305,0.006847305,0.006847305,0.006847305,0.000000000],[0.006847305,0.006847305,0.125512130,0.006847305,0.000000000],[0.006847305,0.778625602,0.006847305,0.006847305,0.000000000],[0.006847305,0.006847305,0.006847305,0.006847305,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|G|43 - 4V9F|1|9|C|46 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.863636364,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4V9F|1|9|A|44
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.755319149,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.010638298,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.010638298,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.223404255,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4V9F|1|9|A|45
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
