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 G1500 - C1516 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G1500 - C1516 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000390625000000000090000000000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [2] | Right Index [9] | Norm Constant [0.000838322805523] // Cluster node U1501:C1505 and G1513:A1515
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.017042123,0.002977202,0.037605848,0.002977202,0.000000000],[0.276030134,0.013421133,0.307621142,0.002977202,0.000000000],[0.002977202,0.002977202,0.014455549,0.023565365,0.000000000],[0.019762200,0.002977202,0.013381459,0.259251838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1502 - G1513 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1505 - G1513 cWW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.176024722,0.017524598,0.011968742,0.007361925,0.000000000],[0.177887855,0.012464556,0.015288477,0.008315159,0.000000000],[0.157441102,0.012725025,0.159911912,0.006187823,0.000000000],[0.206137050,0.014365445,0.009707613,0.006687996,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1501 - A1515 cSW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.245658821,0.209574587,0.193047757,0.211475948,0.000000000],[0.014488228,0.011537871,0.011728843,0.011782382,0.000000000],[0.011147315,0.011695357,0.025480784,0.011026475,0.000000000],[0.008114098,0.009266432,0.006590193,0.007384909,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1504 - A1515 cWS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.121142655,0.120842989,0.006476604,0.005755261,0.000000000],[0.144971527,0.110518240,0.001350705,0.112517076,0.000000000],[0.006512780,0.006422996,0.011124298,0.109338445,0.000000000],[0.016481658,0.116826263,0.001350705,0.108367796,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1502 - A1504 cSH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.199738643,0.010889283,0.002471564,0.013930491,0.000000000],[0.011522819,0.257057341,0.019747221,0.022305949,0.000000000],[0.011507868,0.026066064,0.002471564,0.009842358,0.000000000],[0.165962880,0.222962299,0.013113694,0.010409963,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1502 - C1505 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1503
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.785714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1514
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 [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
