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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000000006156681] | Pair Probability [[0.008854514,0.016740477,0.009873999,0.189704501,0.000000000],[0.020645154,0.009422516,0.212263396,0.011508821,0.000000000],[0.009925891,0.189884907,0.001981704,0.022312113,0.000000000],[0.233465652,0.010917253,0.042775962,0.009723142,0.000000000],[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 [0.000000000,0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.535714286,0.035714286,0.392857143,0.035714286,0.000000000] | Left Index [1] | Right Index [11] // Basepair C774 - G887 cWW 
JunctionNode | Branches [2]  | Left Index [2] | Right Index [10] // Junction node G775 - C884 ID J8234
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.222222222,0.222222222,0.333333333,0.222222222,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Initial node 4V9F|1|0|G|775 - 4V9F|1|0|U|866 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 4V9F|1|0|G|775
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 [3] | Right Index [7] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000015557317266020809512875033260945487973765004666] | Num Left Bases [4] | Num Right Bases [1] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Cluster node 4V9F|1|0|A|776:4V9F|1|0|A|780 and 4V9F|1|0|U|866:4V9F|1|0|U|866
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.008932627,0.021179957,0.009540239,0.253016483,0.000000000],[0.016857107,0.009218740,0.186838956,0.009967940,0.000000000],[0.009521668,0.189261136,0.001964127,0.051205712,0.000000000],[0.188626503,0.010612004,0.022144213,0.011112588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|A|780 - 4V9F|1|0|U|866 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.014891944,0.013905790,0.002823376,0.338941367,0.000000000],[0.013878528,0.014035418,0.002823376,0.121062079,0.000000000],[0.013652211,0.002823376,0.002823376,0.013741685,0.000000000],[0.013159833,0.028084494,0.132673385,0.270679762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|A|776 - 4V9F|1|0|U|779 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.015625000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.953125000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|0|C|778
Insertion    | Location [1] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.187500000,0.062500000,0.312500000,0.437500000,0.000000000]// Insertion after nucleotide 3, position 1 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 [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
InitialNode  | Left Length Distribution [1.000000000] | 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 [8] | Right Index [10] // Initial node 4V9F|1|0|A|867 - 4V9F|1|0|C|884 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.687500000,0.062500000,0.187500000,0.062500000,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 4V9F|1|0|U|866
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 [9] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair G868 - C884 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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
