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 [7] // Initial node C2680 - G2727 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000146283685379421310000000000000000000000000] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.008888954407175] // Cluster node C2680:U2684 and A2725:G2727
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.016212895,0.002088714,0.111481584,0.002088714,0.000000000],[0.355482037,0.009855145,0.215225219,0.002088714,0.000000000],[0.002088714,0.014532442,0.014015048,0.021263925,0.000000000],[0.020326329,0.014532442,0.009960906,0.188757171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2681 - A2725 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.007773162,0.016660361,0.008500029,0.171131704,0.000000000],[0.019645867,0.007811276,0.181182794,0.009165013,0.000000000],[0.008511496,0.180416929,0.001800083,0.020080857,0.000000000],[0.324199513,0.009115154,0.022960409,0.011045352,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2684 - A2725 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.008273910,0.016324110,0.009447193,0.172538687,0.000000000],[0.016686769,0.007282678,0.238983699,0.010738157,0.000000000],[0.009443468,0.247301898,0.001797856,0.021312961,0.000000000],[0.198008406,0.010754857,0.021649574,0.009455779,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2680 - G2727 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.069820510,0.113337012,0.066293327,0.077837807,0.000000000],[0.136330573,0.145599904,0.162841133,0.111769004,0.000000000],[0.010416831,0.009184966,0.054902910,0.007662833,0.000000000],[0.009188309,0.009573906,0.007480149,0.007760825,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2683 - G2727 cWS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.088151994,0.087434743,0.005896706,0.004967894,0.000000000],[0.146654711,0.205693479,0.013917998,0.094278770,0.000000000],[0.041390756,0.005358183,0.009542222,0.094186828,0.000000000],[0.021244251,0.084343406,0.001266537,0.095671523,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2681 - C2683 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.104166667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.145833333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U2682
Insertion    | Location [2] | Length Distribution [0.906945833,0.092734748,0.000309116,0.000010304] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [6] | Length Distribution [0.182283898,0.544177099,0.272829207,0.000678936,0.000030861] | Letter Distribution [0.442307692,0.250000000,0.173076923,0.134615385,0.000000000]// Insertion after nucleotide 6, position 6 in cluster node
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 [6] | Right Index [5] // New Initial node after Cluster
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
