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 [22] // 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 [22] // 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 [21] // Fixed node on right for 8K85|1|B|U|49
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 [20] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000150613574911793666666304] | Num Left Bases [8] | Num Right Bases [5] | Left Index [2] | Right Index [20] | Norm Constant [0.042106869219010] // Cluster node 8K85|1|B|G|41:8K85|1|B|G|50 and 8K85|1|A|G|7:8K85|1|A|G|12
Interaction  | Interacting Bases [3,9] | Pair Probability [[0.004732165,0.004732165,0.048667733,0.040090134,0.000000000],[0.004732165,0.050159009,0.004732165,0.017067191,0.000000000],[0.196762814,0.004732165,0.529820255,0.004732165,0.000000000],[0.016355421,0.004732165,0.014803301,0.053148989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|44 - 8K85|1|A|G|7 cWH 
Interaction  | Interacting Bases [1,10] | Pair Probability [[0.001219366,0.001219366,0.012540512,0.010330270,0.000000000],[0.001219366,0.012924778,0.001219366,0.004397807,0.000000000],[0.253505381,0.006096829,0.666286682,0.006096829,0.000000000],[0.004214401,0.001219366,0.003814457,0.013695225,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|41 - 8K85|1|A|G|8 cWH 
Interaction  | Interacting Bases [8,11] | 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]] // Cluster Interaction 8K85|1|B|G|50 - 8K85|1|A|C|10 cWW 
Interaction  | Interacting Bases [6,12] | 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 [5,13] | 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 [[0.000333199,0.000333199,0.069271890,0.001151611,0.000000000],[0.000333199,0.003531774,0.001665996,0.000333199,0.000000000],[0.017133857,0.001665996,0.889601625,0.005211618,0.000000000],[0.002822809,0.001201728,0.001665996,0.003742304,0.000000000],[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 [[0.000942582,0.000813813,0.000168455,0.113049415,0.000000000],[0.000822289,0.001011382,0.000168455,0.094866045,0.000000000],[0.000808931,0.000168455,0.000168455,0.005814680,0.000000000],[0.003926562,0.009840102,0.035471773,0.731958608,0.000000000],[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 [9,12] | Pair Probability [[0.004732165,0.004732165,0.048667733,0.040090134,0.000000000],[0.004732165,0.050159009,0.004732165,0.017067191,0.000000000],[0.196762814,0.004732165,0.529820255,0.004732165,0.000000000],[0.016355421,0.004732165,0.014803301,0.053148989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|A|G|7 - 8K85|1|A|G|11 cWH 
Interaction  | Interacting Bases [10,13] | Pair Probability [[0.004732165,0.004732165,0.048667733,0.040090134,0.000000000],[0.004732165,0.050159009,0.004732165,0.017067191,0.000000000],[0.196762814,0.004732165,0.529820255,0.004732165,0.000000000],[0.016355421,0.004732165,0.014803301,0.053148989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|A|G|8 - 8K85|1|A|G|12 cWH 
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
Insertion    | Location [10] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.312500000,0.062500000,0.062500000,0.562500000,0.000000000]// Insertion after nucleotide 17, position 10 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 [10] | Right Index [15] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.249153714,0.021920143,0.024885446,0.124177707,0.000000000],[0.016670575,0.009303910,0.125178380,0.017438416,0.000000000],[0.020436395,0.157035067,0.031362300,0.026124160,0.000000000],[0.122430467,0.018976185,0.020925698,0.013981436,0.000000000],[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 [10] | Right Index [15] // Basepair G51 - C6 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.022071540,0.013806419,0.334911111,0.016898899,0.000000000],[0.014138398,0.009771948,0.018493445,0.043420140,0.000000000],[0.405193794,0.018288065,0.003485900,0.015053859,0.000000000],[0.016931858,0.041094913,0.015383423,0.011056290,0.000000000],[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 [11] | Right Index [14] // Basepair G52 - A5 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[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 [12] | Right Index [13] // Basepair C53 - G4 cWW 
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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
