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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | 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]] | 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 [1] | Right Index [14] // Basepair A40 - U14 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Position [2] | Left Index [2] | Right Index [13] // Fixed node on right for 8K85|1|B|U|47
InitialNode  | Left Length Distribution [1.000000000] | 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 [2] | Right Index [12] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000000048406024103125380564744386755250783] | Num Left Bases [7] | Num Right Bases [2] | Left Index [2] | Right Index [12] | Norm Constant [0.674377293971866] // Cluster node 8K85|1|B|G|41:8K85|1|B|U|49 and 8K85|1|A|G|11:8K85|1|A|G|12
Interaction  | Interacting Bases [6,8] | Pair Probability [[0.001435895,0.001435895,0.059704349,0.004962776,0.000000000],[0.001435895,0.015219903,0.001435895,0.001435895,0.000000000],[0.073837003,0.007179477,0.774551476,0.022459058,0.000000000],[0.012164673,0.005178750,0.001435895,0.016127162,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|48 - 8K85|1|A|G|11 cHW 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.001435895,0.001435895,0.059704349,0.004962776,0.000000000],[0.001435895,0.015219903,0.001435895,0.001435895,0.000000000],[0.073837003,0.007179477,0.774551476,0.022459058,0.000000000],[0.012164673,0.005178750,0.001435895,0.016127162,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|46 - 8K85|1|A|G|12 cHW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.001219366,0.001219366,0.253505381,0.004214401,0.000000000],[0.001219366,0.012924778,0.006096829,0.001219366,0.000000000],[0.012540512,0.001219366,0.666286682,0.003814457,0.000000000],[0.010330270,0.004397807,0.006096829,0.013695225,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|41 - 8K85|1|B|G|46 cHW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.001219366,0.001219366,0.253505381,0.004214401,0.000000000],[0.001219366,0.012924778,0.006096829,0.001219366,0.000000000],[0.012540512,0.001219366,0.666286682,0.003814457,0.000000000],[0.010330270,0.004397807,0.006096829,0.013695225,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|44 - 8K85|1|B|G|48 cHW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.002332550,0.002013893,0.000416865,0.279756455,0.000000000],[0.002034867,0.002502804,0.000416865,0.234759185,0.000000000],[0.002001813,0.000416865,0.000416865,0.014389233,0.000000000],[0.001943364,0.004870140,0.017555964,0.434172274,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|U|42 - 8K85|1|B|U|49 tSW 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8K85|1|B|U|45
Insertion    | Location [2] | 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 2 in cluster node
Insertion    | Location [5] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000]// Insertion after nucleotide 6, position 5 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 [9] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 [9] | Right Index [10] // Basepair G50 - C10 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
