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
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011246147,0.013983971,0.014277598,0.037274594,0.000000000],[0.302538153,0.027950744,0.042354115,0.016034133,0.000000000],[0.014590167,0.037125289,0.003306148,0.014672010,0.000000000],[0.086192816,0.014679149,0.350222612,0.013552354,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair U553 - G538 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.254054619,0.030817459,0.003085436,0.078069718,0.000000000],[0.051066155,0.022009051,0.001180361,0.001180361,0.000000000],[0.056885153,0.003996729,0.365987125,0.035619494,0.000000000],[0.047237901,0.046449718,0.001180361,0.001180361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [14] // Basepair A554 - A537 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000001904521072278912302090434780238574181827] | Num Left Bases [4] | Num Right Bases [3] | Left Index [3] | Right Index [13] | Norm Constant [0.004275561412192] // Cluster node 8P9A|1|AR|U|555:8P9A|1|AR|A|559 and 8P9A|1|AR|A|533:8P9A|1|AR|U|536
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|555 - 8P9A|1|AR|A|533 tWH 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.615264647,0.027680686,0.049320315,0.027089794,0.000000000],[0.018530781,0.010338068,0.027182752,0.026285801,0.000000000],[0.037714972,0.027750896,0.005956568,0.029081265,0.000000000],[0.026324389,0.029605623,0.020261781,0.021611660,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|559 - 8P9A|1|AR|A|533 cWW 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.003068279,0.003068279,0.011304130,0.326435762,0.000000000],[0.003068279,0.014755072,0.003068279,0.003068279,0.000000000],[0.013222312,0.003068279,0.010604660,0.283904858,0.000000000],[0.013284346,0.290617672,0.003068279,0.014393233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|557 - 8P9A|1|AR|U|536 cHW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.076635853,0.076984536,0.004307628,0.077941519,0.000000000],[0.076263771,0.087816675,0.000950558,0.078833738,0.000000000],[0.077619343,0.000950558,0.079946321,0.090505528,0.000000000],[0.078194836,0.077434927,0.000950558,0.114663652,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|555 - 8P9A|1|AR|U|556 cSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.003068279,0.003068279,0.013222312,0.013284346,0.000000000],[0.003068279,0.014755072,0.003068279,0.290617672,0.000000000],[0.011304130,0.003068279,0.010604660,0.003068279,0.000000000],[0.326435762,0.003068279,0.283904858,0.014393233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|556 - 8P9A|1|AR|A|559 cWH 
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|535 - 8P9A|1|AR|U|536 cSH 
Insertion    | Location [3] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 5, position 3 in cluster node
Insertion    | Location [5] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 11, position 5 in cluster node
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.022937090,0.014347847,0.348044880,0.017561601,0.000000000],[0.014692845,0.010155161,0.019218678,0.045122890,0.000000000],[0.381868061,0.019005244,0.003622602,0.015644206,0.000000000],[0.017595852,0.042706478,0.015986694,0.011489870,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair G560 - A532 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [8] | Right Index [9] // Basepair C561 - G531 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
