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 [8] // Initial node A2520 - U2587 from junction 
BasepairNode | Deletion Probability [0.0000000005912491] | Pair Probability [[0.009722986,0.022602524,0.010807110,0.213946067,0.000000000],[0.018642384,0.008854915,0.200306720,0.011770232,0.000000000],[0.010724456,0.213953122,0.002148800,0.027678057,0.000000000],[0.199554445,0.012136228,0.023684855,0.013467100,0.000000000],[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 [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.083333333,0.083333333,0.583333333,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair A2520 - U2587 cWW 
ClusterNode  | Deletion Probability [0.000000000000000077146797411633740000000000000000000000000000] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Cluster node U2521:C2526 and G2584:G2584
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009640843,0.020820542,0.010733993,0.213406915,0.000000000],[0.020428208,0.008935347,0.213416622,0.012101297,0.000000000],[0.010799946,0.200886051,0.002149018,0.025786435,0.000000000],[0.200132635,0.011807914,0.025581673,0.013372561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2526 - G2584 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.007512069,0.008360159,0.007186863,0.008188381,0.000000000],[0.014137583,0.014479854,0.010969251,0.014468650,0.000000000],[0.010578210,0.009148700,0.008845779,0.007931851,0.000000000],[0.327000080,0.177983196,0.181398224,0.191811151,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2521 - A2523 cWS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A2524
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G2525
Insertion    | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 1 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 [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
