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 [10] // Initial node U2636 - G2782 from junction 
BasepairNode | Deletion Probability [0.0000000082449969] | Pair Probability [[0.011568670,0.015004905,0.013717942,0.086563999,0.000000000],[0.210007908,0.013051939,0.116859137,0.015670913,0.000000000],[0.013991452,0.091895298,0.002952919,0.017566300,0.000000000],[0.091345969,0.014368361,0.272912695,0.012521592,0.000000000],[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 [0.493624023,0.004113534,0.004319210,0.493624023,0.004113534,0.000205677] | Right Letter Distribution [0.409090909,0.045454545,0.318181818,0.227272727,0.000000000] | Left Index [1] | Right Index [10] // Basepair U2636 - G2782 cWW 
ClusterNode  | Deletion Probability [0.0000000000425867] | Num Left Bases [2] | Num Right Bases [2] | Left Index [2] | Right Index [9] | Norm Constant [0.135108635236567] // Cluster node U2637:G2638 and A2776:A2778
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.022193440,0.004032174,0.068294143,0.004032174,0.000000000],[0.144395317,0.030088333,0.108454026,0.004032174,0.000000000],[0.031964102,0.004032174,0.042564995,0.024183430,0.000000000],[0.346043401,0.004032174,0.042578165,0.119079776,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2637 - A2776 tWH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.118423907,0.109714818,0.001277960,0.007504879,0.000000000],[0.140269246,0.096413576,0.001277960,0.001277960,0.000000000],[0.122838246,0.001277960,0.008044388,0.043009991,0.000000000],[0.232162706,0.113950484,0.001277960,0.001277960,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2637 - A2778 tSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.211954656,0.114102715,0.001179443,0.005616359,0.000000000],[0.098760399,0.103515300,0.001179443,0.001179443,0.000000000],[0.146246221,0.001179443,0.005714155,0.098106004,0.000000000],[0.106402395,0.102505136,0.001179443,0.001179443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2638 - A2778 tSH 
Insertion    | Location [3] | Length Distribution [0.497737557,0.497737557,0.004319210,0.000205677] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000]// Insertion after nucleotide 8, position 3 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 [4] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.143107073,0.122479494,0.173101272,0.122989924,0.000000000],[0.118256878,0.083202990,0.001347441,0.118428795,0.000000000],[0.001347441,0.001347441,0.009331305,0.001347441,0.000000000],[0.008716688,0.001347441,0.060405157,0.033243218,0.000000000],[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 [4] | Right Index [7] // Basepair A2639 - A2775 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010795257,0.065846457,0.011939594,0.162136419,0.000000000],[0.016688363,0.008619217,0.183721697,0.013216907,0.000000000],[0.011812838,0.216159781,0.002277618,0.086324791,0.000000000],[0.160516374,0.013801104,0.022111314,0.014032271,0.000000000],[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 [5] | Right Index [6] // Basepair G2640 - C2774 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
