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 [31] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [31] // Basepair C119 - G222 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Position [2] | Left Index [2] | Right Index [30] // Fixed node on right for 1U9S|1|A|A|220
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [29] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [2] | Right Index [29] // Junction node A120 - A220 ID J6557
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [20] // Initial node 1U9S|1|A|A|120 - 1U9S|1|A|A|174 from node 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000029793021831941294771334241] | Num Left Bases [9] | Num Right Bases [5] | Left Index [2] | Right Index [20] | Norm Constant [0.001190246544109] // Cluster node 1U9S|1|A|A|120:1U9S|1|A|A|129 and 1U9S|1|A|U|170:1U9S|1|A|A|174
Interaction  | Interacting Bases [3,10] | Pair Probability [[0.076146696,0.078906659,0.078575452,0.093178774,0.000000000],[0.074822471,0.079495189,0.003326749,0.073057805,0.000000000],[0.076666471,0.003253861,0.009031637,0.075892455,0.000000000],[0.069121724,0.064122585,0.069548293,0.074853180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|122 - 1U9S|1|A|U|170 cSS 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.071773872,0.083480414,0.634367958,0.077201799,0.000000000],[0.071430006,0.003933530,0.006244670,0.003877011,0.000000000],[0.000892096,0.000892096,0.006244670,0.007019357,0.000000000],[0.004313658,0.003566586,0.020478373,0.004283906,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|126 - 1U9S|1|A|G|171 tWS 
Interaction  | Interacting Bases [1,12] | Pair Probability [[0.383941828,0.060098347,0.003586629,0.003659217,0.000000000],[0.329063595,0.000748082,0.063774503,0.007108337,0.000000000],[0.018648642,0.062959472,0.001867211,0.000748082,0.000000000],[0.025405115,0.036894776,0.000748082,0.000748082,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|120 - 1U9S|1|A|A|172 tHH 
Interaction  | Interacting Bases [4,14] | Pair Probability [[0.071773872,0.071430006,0.000892096,0.004313658,0.000000000],[0.083480414,0.003933530,0.000892096,0.003566586,0.000000000],[0.634367958,0.006244670,0.006244670,0.020478373,0.000000000],[0.077201799,0.003877011,0.007019357,0.004283906,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|G|123 - 1U9S|1|A|A|174 tSW 
Interaction  | Interacting Bases [9,14] | Pair Probability [[0.207494268,0.188108213,0.192542081,0.181451180,0.000000000],[0.001975933,0.001975933,0.020316853,0.001975933,0.000000000],[0.016360862,0.001975933,0.016877025,0.161042056,0.000000000],[0.001975933,0.001975933,0.001975933,0.001975933,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|129 - 1U9S|1|A|A|174 tSS 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.375057930,0.003651569,0.322134033,0.003651569,0.000000000],[0.031255259,0.015495970,0.003651569,0.003651569,0.000000000],[0.003651569,0.009045434,0.134222277,0.039085253,0.000000000],[0.016500420,0.003651569,0.017501970,0.017792036,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|122 - 1U9S|1|A|A|126 tWH 
Interaction  | Interacting Bases [6,9] | Pair Probability [[0.083071528,0.077827995,0.079676854,0.073574035,0.000000000],[0.086320773,0.084839186,0.003406498,0.011604013,0.000000000],[0.099703595,0.003481632,0.007719409,0.061927698,0.000000000],[0.084731846,0.078131797,0.078751916,0.085231224,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|G|125 - 1U9S|1|A|A|129 cSS 
Interaction  | Interacting Bases [10,14] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|U|170 - 1U9S|1|A|A|174 tWH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.013513514,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.959459459,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1U9S|1|A|C|121
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1U9S|1|A|A|124
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1U9S|1|A|A|127
Interaction  | Interacting Bases [13,13] | Pair Probability [[0.959459459,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 1U9S|1|A|A|173
Insertion    | Location [8] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 9, position 8 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [15] // Initial node 1U9S|1|A|G|130 - 1U9S|1|A|G|169 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [11] | Right Index [15] // Fixed node on left for 1U9S|1|A|A|129
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [12] | Right Index [15] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [2] | Left Index [12] | Right Index [15] // Fixed node on right for 1U9S|1|A|G|168
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [14] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [12] | Right Index [14] | Norm Constant [0.290489050332303] // Cluster node 1U9S|1|A|A|131:1U9S|1|A|C|132 and 1U9S|1|A|G|168:1U9S|1|A|G|168
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.004741436,0.008502533,0.005450864,0.098834917,0.000000000],[0.050405519,0.024145075,0.529397411,0.034282440,0.000000000],[0.005512079,0.100964543,0.001038993,0.011667026,0.000000000],[0.100116212,0.006606094,0.013310241,0.005024617,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|C|132 - 1U9S|1|A|G|168 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|A|131 - 1U9S|1|A|C|132 cSH 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [13] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [14] | Right Index [14] | 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 [21] | Right Index [29] // Initial node 1U9S|1|A|C|175 - 1U9S|1|A|A|220 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [21] | Right Index [29] // Fixed node on left for 1U9S|1|A|A|174
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [22] | Right Index [29] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [22] | Right Index [29] // Junction node G176 - A220 ID J357
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [22] | Right Index [23] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[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 [22] | Right Index [23] // Basepair G176 - C194 cWW 
HairpinNode  | Num Bases [1] | Left Index [23] | Right Index [23] | 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 [24] | Right Index [29] // Initial node 1U9S|1|A|G|195 - 1U9S|1|A|A|220 from node 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [2] | Num Right Bases [4] | Left Index [24] | Right Index [29] | Norm Constant [0.250280977299386] // Cluster node 1U9S|1|A|G|195:1U9S|1|A|C|196 and 1U9S|1|A|G|217:1U9S|1|A|A|220
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|C|196 - 1U9S|1|A|G|217 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|G|195 - 1U9S|1|A|C|219 cWW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.218661090,0.014620617,0.019969329,0.007807710,0.000000000],[0.206663216,0.011999471,0.002249461,0.008266368,0.000000000],[0.234847085,0.002249461,0.027362667,0.006356246,0.000000000],[0.208475927,0.012213416,0.010584145,0.007673792,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1U9S|1|A|G|217 - 1U9S|1|A|A|220 cSW 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 1U9S|1|A|G|218
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [26] | Right Index [25] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [26] | Right Index [26] | 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
