Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [15] // Initial node G531 - C561 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[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 [15] // Basepair G531 - C561 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.315343748,0.019630589,0.493904012,0.022103230,0.000000000],[0.003833930,0.001478680,0.005249063,0.011169182,0.000000000],[0.093002083,0.005315980,0.000968006,0.004364346,0.000000000],[0.004413113,0.011881031,0.004267756,0.003075251,0.000000000],[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 [2] | Right Index [14] // Basepair A532 - G560 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000001861482761166059500000000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [13] | Norm Constant [0.002186805502869] // Cluster node A533:U536 and U555:A559
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.026228946,0.054639536,0.005500826,0.559983562,0.000000000],[0.005500826,0.045670107,0.005500826,0.005500826,0.000000000],[0.026982756,0.036513624,0.064376936,0.067861159,0.000000000],[0.005500826,0.005500826,0.025659745,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A533 - U555 tHW 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.011713255,0.098795318,0.001115418,0.005321145,0.000000000],[0.103847303,0.005193506,0.005039138,0.004579369,0.000000000],[0.567609822,0.151988445,0.005577088,0.018128417,0.000000000],[0.006756583,0.004694656,0.006215599,0.003424936,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G535 - A557 tSW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U536 - A557 cWH 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.738708947,0.033322493,0.007288080,0.007288080,0.000000000],[0.027777766,0.025772735,0.007288080,0.007288080,0.000000000],[0.007288080,0.007288080,0.058183744,0.043353518,0.000000000],[0.007288080,0.007288080,0.007288080,0.007288080,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A533 - A559 bif 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.066577006,0.068586257,0.003740469,0.003094775,0.000000000],[0.064400289,0.074806542,0.000795565,0.075390323,0.000000000],[0.032523262,0.017785442,0.036355651,0.407683380,0.000000000],[0.005728730,0.066713376,0.000795565,0.075023369,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G535 - U536 cSH 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.111957140,0.109553485,0.005904964,0.004876169,0.000000000],[0.106210408,0.127560275,0.001323815,0.126229679,0.000000000],[0.010119885,0.005598590,0.008485208,0.124838481,0.000000000],[0.007055763,0.106679783,0.001323815,0.142282540,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U555 - U556 cSH 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U556 - A559 cWH 
Insertion    | Location [1] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
Insertion    | Location [6] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 12, position 6 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 [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.170710115,0.155925473,0.133465681,0.148228098,0.000000000],[0.128906975,0.063872294,0.001608091,0.142674762,0.000000000],[0.001608091,0.001608091,0.013969090,0.001608091,0.000000000],[0.012727400,0.001608091,0.019871564,0.001608091,0.000000000],[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 [6] | Right Index [9] // Basepair A537 - A554 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016663800,0.313360908,0.015725272,0.045114411,0.000000000],[0.014618495,0.011663950,0.038590886,0.015584762,0.000000000],[0.015377247,0.044737484,0.003487844,0.358685405,0.000000000],[0.038297587,0.017266078,0.015312095,0.035513776,0.000000000],[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 [7] | Right Index [8] // Basepair G538 - U553 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
