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 [15] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000009702767374778475363395556941852770237] | Num Left Bases [6] | Num Right Bases [3] | Left Index [1] | Right Index [15] | Norm Constant [0.032273280081773] // Cluster node 4LFB|1|A|C|1296:4LFB|1|A|U|1301 and 4LFB|1|A|A|1238:4LFB|1|A|G|1241
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.006184437,0.001368626,0.006423550,0.001368626,0.000000000],[0.013763337,0.110285091,0.001368626,0.001368626,0.000000000],[0.001368626,0.003280687,0.010408284,0.006087177,0.000000000],[0.722774475,0.006843129,0.039703016,0.067403687,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|U|1301 - 4LFB|1|A|A|1238 tWH 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|C|1296 - 4LFB|1|A|G|1241 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.076237190,0.077111654,0.004252175,0.075410848,0.000000000],[0.070394979,0.107013790,0.000906783,0.066471944,0.000000000],[0.065758608,0.000906783,0.079025844,0.135385670,0.000000000],[0.077861399,0.077702655,0.000906783,0.084652893,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|C|1297 - 4LFB|1|A|C|1298 cSH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.037023816,0.037725570,0.002074269,0.036868680,0.000000000],[0.027640698,0.041655016,0.000459278,0.077578724,0.000000000],[0.161738926,0.002296392,0.197293920,0.258485305,0.000000000],[0.037598275,0.037372567,0.000459278,0.043729285,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|1300 - 4LFB|1|A|U|1301 cSH 
Interaction  | Interacting Bases [7,9] | Pair Probability [[0.080675234,0.083830751,0.125673684,0.082287658,0.000000000],[0.075582957,0.082391902,0.003381201,0.075877995,0.000000000],[0.077378483,0.003308233,0.007496734,0.076480226,0.000000000],[0.071451707,0.011269282,0.060141322,0.082772631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|1238 - 4LFB|1|A|G|1241 cSS 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|A|1299
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4LFB|1|A|A|1239
Insertion    | Location [8] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000]// Insertion after nucleotide 14, position 8 in cluster node
InitialNode  | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.250000000,0.250000000,0.416666667,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [12] // Initial node 4LFB|1|A|C|1303 - 4LFB|1|A|C|1237 from node 
JunctionNode | Branches [2]  | Left Index [7] | Right Index [12] // Junction node C1303 - C1237 ID J7060
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.003195009,0.006420112,0.007364406,0.066212977,0.000000000],[0.016223489,0.008103525,0.698620810,0.011440025,0.000000000],[0.003627320,0.078056692,0.001397981,0.008551763,0.000000000],[0.065799686,0.004506885,0.017098952,0.003380369,0.000000000],[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 [7] | Right Index [8] // Basepair C1303 - G1334 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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 [9] | Right Index [12] // Initial node 4LFB|1|A|C|1335 - 4LFB|1|A|C|1237 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.250000000,0.250000000,0.000000000] | Position [1] | Left Index [9] | Right Index [12] // Fixed node on left for 4LFB|1|A|A|1299
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [10] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.716666667,0.016666667,0.016666667,0.000000000] | Position [1] | Left Index [10] | Right Index [12] // Fixed node on left for 4LFB|1|A|G|1300
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [11] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.005225246,0.010882317,0.005950161,0.108073126,0.000000000],[0.009178287,0.005123879,0.108988879,0.007131125,0.000000000],[0.025063277,0.516194323,0.004777328,0.061200985,0.000000000],[0.106689997,0.007401420,0.012594283,0.005525367,0.000000000],[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 [11] | Right Index [12] // Basepair G1337 - C1237 cWW 
HairpinNode  | Num Bases [1] | Left Index [12] | Right Index [12] | 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
