Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [14] // Initial node U1247 - G1290 from junction 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.011606602,0.017778352,0.013679584,0.116107298,0.000000000],[0.167090224,0.012234263,0.126818052,0.015364421,0.000000000],[0.013781309,0.136797428,0.002838808,0.021529953,0.000000000],[0.118996443,0.014843715,0.198100860,0.012432686,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair U1247 - G1290 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [2] | Right Index [13] | Norm Constant [0.096189158088804] // Cluster node A1248:C1249 and A1288:A1289
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.116980406,0.002286289,0.128092864,0.002286289,0.000000000],[0.238432839,0.010818673,0.211972452,0.002286289,0.000000000],[0.002286289,0.002286289,0.015616865,0.023612565,0.000000000],[0.022709642,0.002286289,0.010943960,0.207102000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1248 - A1288 tWH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.116980406,0.002286289,0.128092864,0.002286289,0.000000000],[0.238432839,0.010818673,0.211972452,0.002286289,0.000000000],[0.002286289,0.002286289,0.015616865,0.023612565,0.000000000],[0.022709642,0.002286289,0.010943960,0.207102000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1249 - A1288 tWH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.372110072,0.003623062,0.310683039,0.003623062,0.000000000],[0.127534032,0.013309690,0.020739161,0.003623062,0.000000000],[0.003623062,0.003623062,0.044878779,0.032327470,0.000000000],[0.017275422,0.003623062,0.021448740,0.017955228,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1248 - A1289 tWH 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [11] // Initial node A1250 - A1287 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [11] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [5] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [11] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [6] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [6] | Right Index [11] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [2] | Left Index [6] | Right Index [10] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.209900785,0.189444278,0.003757542,0.029684459,0.000000000],[0.026190026,0.016148501,0.011187579,0.015892215,0.000000000],[0.003757542,0.013137060,0.191703579,0.206023018,0.000000000],[0.017467990,0.015584336,0.018297597,0.031823494,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A1252 - A1285 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009722986,0.022602524,0.010807110,0.213946067,0.000000000],[0.018642384,0.008854915,0.200306720,0.011770232,0.000000000],[0.010724456,0.213953122,0.002148800,0.027678057,0.000000000],[0.199554445,0.012136228,0.023684855,0.013467100,0.000000000],[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 G1253 - C1284 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
