Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000122368629759416866559708989908376050276] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [10] | Norm Constant [0.000067041245439] // Cluster node 5J7L|1|AA|G|1144:5J7L|1|AA|U|1148 and 5J7L|1|AA|U|1125:5J7L|1|AA|C|1128
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.027924827,0.003262473,0.093329234,0.102192954,0.000000000],[0.336051234,0.023769222,0.003262473,0.003262473,0.000000000],[0.003262473,0.011390225,0.029337962,0.030072816,0.000000000],[0.032808466,0.003262473,0.014668147,0.282142548,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|U|1125 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.010153793,0.013295259,0.012926971,0.028012001,0.000000000],[0.336189288,0.037265996,0.031668407,0.014435104,0.000000000],[0.013237803,0.026709543,0.003263854,0.013805080,0.000000000],[0.035195420,0.013154930,0.298667921,0.112018631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|U|1148 - 5J7L|1|AA|U|1125 cWW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.027077160,0.013263515,0.336823218,0.015884116,0.000000000],[0.111882560,0.008821255,0.017156401,0.038551963,0.000000000],[0.314186837,0.017349072,0.003270193,0.014431498,0.000000000],[0.015853196,0.040733305,0.014122327,0.010593386,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|G|1127 cWW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|G|1144 - 5J7L|1|AA|C|1128 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.015946486,0.021094317,0.014190945,0.019217607,0.000000000],[0.250280716,0.285636061,0.002660282,0.256139873,0.000000000],[0.023389228,0.002660282,0.028048170,0.010653057,0.000000000],[0.016345983,0.026420949,0.012444452,0.014871593,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|C|1147 - 5J7L|1|AA|C|1128 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.149957916,0.149239472,0.001863865,0.009012572,0.000000000],[0.174416518,0.008218366,0.001863865,0.007451707,0.000000000],[0.295120901,0.001863865,0.001863865,0.006112240,0.000000000],[0.161298541,0.008100281,0.014665616,0.008950410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|G|1144 - 5J7L|1|AA|A|1146 tSW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.073487471,0.172991129,0.004089809,0.072451280,0.000000000],[0.074228657,0.095370878,0.000855670,0.059533332,0.000000000],[0.062984968,0.000855670,0.075123456,0.077606387,0.000000000],[0.075261748,0.075253413,0.000855670,0.079050462,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|C|1147 cSH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.030266179,0.014471746,0.003677806,0.117213399,0.000000000],[0.016804021,0.377584550,0.003677806,0.024981981,0.000000000],[0.016216603,0.003677806,0.003677806,0.014957526,0.000000000],[0.017608979,0.316224142,0.016878549,0.022081100,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|A|1145 - 5J7L|1|AA|U|1148 tSW 
Insertion    | Location [2] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [6] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 8, position 6 in cluster node
InitialNode  | 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 [0.991950402,0.007999600,0.000049998] | 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 [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 C1149 - G1124 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
