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 [11] // Initial node G958 - C1008 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214500000000000000000000] | Num Left Bases [5] | Num Right Bases [4] | Left Index [1] | Right Index [11] | Norm Constant [0.000844173991047] // Cluster node G958:C963 and A1005:C1008
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.020051501,0.002539818,0.142297221,0.002539818,0.000000000],[0.263882817,0.012018367,0.235478309,0.002539818,0.000000000],[0.002539818,0.002539818,0.017348636,0.026230988,0.000000000],[0.025227938,0.002539818,0.012157548,0.230067766,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C959 - A1005 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.012225429,0.015145471,0.014725930,0.034760566,0.000000000],[0.381707213,0.018478793,0.035925510,0.016513221,0.000000000],[0.015080020,0.029754800,0.003718062,0.015583401,0.000000000],[0.042294737,0.014884503,0.334044557,0.015157789,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C963 - A1005 cWW 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.003991852,0.056925429,0.004621971,0.075754404,0.000000000],[0.006735384,0.023040960,0.081591292,0.005193253,0.000000000],[0.004563791,0.599043046,0.000841632,0.010795344,0.000000000],[0.075316957,0.038159832,0.009312144,0.004112711,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G958 - C1008 cWW 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.004137439,0.053445697,0.004255207,0.005369948,0.000000000],[0.078512827,0.601694427,0.079760014,0.081014891,0.000000000],[0.004574068,0.027091682,0.006610222,0.003367509,0.000000000],[0.005608553,0.036412329,0.004031225,0.004113960,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C962 - C1008 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.028750495,0.242495727,0.002737822,0.013060892,0.000000000],[0.254895959,0.012747598,0.012368699,0.011240183,0.000000000],[0.283683213,0.074611933,0.002737822,0.008899336,0.000000000],[0.016584213,0.011523157,0.015256354,0.008406597,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G958 - A961 tSW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.111414184,0.110164164,0.006015482,0.005004925,0.000000000],[0.107770754,0.141613670,0.001317127,0.123910582,0.000000000],[0.011483518,0.005613507,0.009660713,0.123848748,0.000000000],[0.007736315,0.106213420,0.001317127,0.126915765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C959 - C962 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 C959 - C963 tSW 
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1006
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1007
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
InitialNode  | 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 [6] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 [6] | Right Index [7] // Basepair G964 - C1004 cWW 
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
