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 [13] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000001944664658252592206548044411245326895476] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [13] | Norm Constant [0.030346452643607] // Cluster node 5J7L|1|DA|C|1043:5J7L|1|DA|A|1048 and 5J7L|1|DA|G|1110:5J7L|1|DA|G|1112
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.042049014,0.042361408,0.409943044,0.046937930,0.000000000],[0.044514549,0.044411471,0.003533393,0.044171708,0.000000000],[0.000504770,0.000504770,0.017273635,0.000504770,0.000000000],[0.002378984,0.000504770,0.299901013,0.000504770,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1048 - 5J7L|1|DA|G|1110 tHS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.057806141,0.057806141,0.057806141,0.057806141,0.000000000],[0.095541990,0.057806141,0.057806141,0.057806141,0.000000000],[0.085738069,0.057806141,0.057806141,0.057806141,0.000000000],[0.067240104,0.057806141,0.057806141,0.057806141,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1044 - 5J7L|1|DA|A|1111 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.108491223,0.114852581,0.001302365,0.006138049,0.000000000],[0.109297235,0.114586629,0.001302365,0.001302365,0.000000000],[0.186840254,0.001302365,0.006366848,0.110539801,0.000000000],[0.121105178,0.113968012,0.001302365,0.001302365,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1047 - 5J7L|1|DA|A|1111 tSH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.009015611,0.016598259,0.010211877,0.190496184,0.000000000],[0.020078202,0.009384364,0.234978378,0.012389530,0.000000000],[0.010297061,0.192647257,0.001996300,0.022446401,0.000000000],[0.213616688,0.011851437,0.034268488,0.009723963,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1043 - 5J7L|1|DA|G|1112 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.242283528,0.165842281,0.236924871,0.157273858,0.000000000],[0.001706013,0.001706013,0.017678100,0.001706013,0.000000000],[0.013376713,0.001706013,0.013932741,0.139039806,0.000000000],[0.001706013,0.001706013,0.001706013,0.001706013,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1048 - 5J7L|1|DA|G|1112 tSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|C|1045
Insertion    | Location [3] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Initial node 5J7L|1|DA|C|1049 - 5J7L|1|DA|C|1109 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.812500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 5J7L|1|DA|A|1048
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.027418842,0.725623265,0.006690195,0.006690195,0.000000000],[0.030801564,0.078351263,0.006690195,0.006690195,0.000000000],[0.006690195,0.006690195,0.028073232,0.006690195,0.000000000],[0.006690195,0.006690195,0.042829885,0.006690195,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair A1050 - C1109 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012304240,0.152595251,0.012221578,0.137557369,0.000000000],[0.014828613,0.010745729,0.115211142,0.013322044,0.000000000],[0.012014775,0.148821138,0.002566200,0.197277540,0.000000000],[0.113221234,0.014204047,0.018215096,0.024894003,0.000000000],[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 [8] | Right Index [9] // Basepair G1051 - U1108 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
