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 G409 - C433 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | 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 [0.991950402,0.007999600,0.000049998] | 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 [1] | Right Index [14] // Basepair G409 - C433 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043716223,0.050956855,0.000526725,0.002508196,0.000000000],[0.044105167,0.046228647,0.000526725,0.000526725,0.000000000],[0.388315159,0.003687073,0.017863095,0.306690455,0.000000000],[0.047517987,0.045777520,0.000526725,0.000526725,0.000000000],[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 [2] | Right Index [13] // Basepair G410 - A432 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000385733987058166880000000000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [12] | Norm Constant [0.409673001779593] // Cluster node A411:A414 and G428:A431
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.004207186,0.005280481,0.062750142,0.005167681,0.000000000],[0.000917983,0.000917983,0.006425879,0.000917983,0.000000000],[0.082535231,0.085064800,0.662195716,0.074439110,0.000000000],[0.000917983,0.000917983,0.006425879,0.000917983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G413 - G428 tSS 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.418144609,0.003985368,0.341751342,0.003985368,0.000000000],[0.031463906,0.014640658,0.022813077,0.003985368,0.000000000],[0.003985368,0.003985368,0.049366656,0.035560217,0.000000000],[0.019002964,0.003985368,0.023593614,0.019750751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A411 - A430 tWH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.418144609,0.031463906,0.003985368,0.019002964,0.000000000],[0.003985368,0.014640658,0.003985368,0.003985368,0.000000000],[0.341751342,0.022813077,0.049366656,0.023593614,0.000000000],[0.003985368,0.003985368,0.035560217,0.019750751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A414 - A430 tHW 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.003460772,0.003460772,0.017164318,0.012348510,0.000000000],[0.003460772,0.037017516,0.016981393,0.188883971,0.000000000],[0.015181754,0.003460772,0.013849500,0.003460772,0.000000000],[0.365685069,0.003460772,0.277303821,0.034819514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U429 - A431 cWH 
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
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 [6] | Right Index [8] // Initial node A415 - U427 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // 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 [7] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[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 G416 - U427 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
