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 [22] // Initial node A8 - U31 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[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 [22] // Basepair A8 - U31 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000000000000000002324854825] | Num Left Bases [10] | Num Right Bases [10] | Left Index [2] | Right Index [21] | Norm Constant [0.021746083431234] // Cluster node G9:U20 and A21:A30
Interaction  | Interacting Bases [6,12] | Pair Probability [[0.021092272,0.036425574,0.004478161,0.208014926,0.000000000],[0.031991796,0.034671284,0.016991909,0.034459906,0.000000000],[0.004478161,0.017978475,0.021445131,0.163657287,0.000000000],[0.043876651,0.031832799,0.038700931,0.289904738,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A15 - U22 tWW 
Interaction  | Interacting Bases [2,13] | Pair Probability [[0.004917740,0.004917740,0.204479002,0.016996810,0.000000000],[0.004917740,0.052126028,0.004917740,0.004917740,0.000000000],[0.050576271,0.004917740,0.511381834,0.015383823,0.000000000],[0.041662297,0.017736492,0.004917740,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G23 cHW 
Interaction  | Interacting Bases [9,13] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G19 - G23 cWH 
Interaction  | Interacting Bases [1,15] | Pair Probability [[0.001267184,0.001267184,0.263446768,0.004379672,0.000000000],[0.001267184,0.013431632,0.006335920,0.001267184,0.000000000],[0.013032297,0.001267184,0.653199885,0.003964044,0.000000000],[0.010735378,0.004570270,0.006335920,0.014232292,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G9 - G25 cHW 
Interaction  | Interacting Bases [8,15] | Pair Probability [[0.001492205,0.001492205,0.076732572,0.012641719,0.000000000],[0.001492205,0.015816762,0.007461025,0.005381839,0.000000000],[0.062045696,0.001492205,0.765710357,0.001492205,0.000000000],[0.005157395,0.001492205,0.023339805,0.016759600,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G18 - G25 cWH 
Interaction  | Interacting Bases [10,17] | Pair Probability [[0.024978059,0.030331969,0.005356900,0.036479807,0.000000000],[0.047086784,0.030567281,0.018993974,0.027347187,0.000000000],[0.005356900,0.018115093,0.025662695,0.038984076,0.000000000],[0.046635242,0.029148575,0.059657587,0.555297871,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U20 - U27 tWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G9 - G13 cWH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.001492205,0.001492205,0.076732572,0.012641719,0.000000000],[0.001492205,0.015816762,0.007461025,0.005381839,0.000000000],[0.062045696,0.001492205,0.765710357,0.001492205,0.000000000],[0.005157395,0.001492205,0.023339805,0.016759600,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G14 cWH 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.004917740,0.004917740,0.050576271,0.041662297,0.000000000],[0.004917740,0.052126028,0.004917740,0.017736492,0.000000000],[0.204479002,0.004917740,0.511381834,0.004917740,0.000000000],[0.016996810,0.004917740,0.015383823,0.055233263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - G18 cWH 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.001267184,0.001267184,0.013032297,0.010735378,0.000000000],[0.001267184,0.013431632,0.001267184,0.004570270,0.000000000],[0.263446768,0.006335920,0.653199885,0.006335920,0.000000000],[0.004379672,0.001267184,0.003964044,0.014232292,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G14 - G19 cWH 
Interaction  | Interacting Bases [11,18] | Pair Probability [[0.431873884,0.331200569,0.019765828,0.020165858,0.000000000],[0.051813191,0.000588951,0.050208540,0.005596268,0.000000000],[0.002936349,0.049566880,0.001470022,0.000588951,0.000000000],[0.004000200,0.029046605,0.000588951,0.000588951,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A21 - A28 tHH 
Interaction  | Interacting Bases [16,19] | 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 G26 - U29 cSH 
Interaction  | Interacting Bases [14,20] | Pair Probability [[0.233349860,0.004938038,0.000525442,0.002449099,0.000000000],[0.233744771,0.002515764,0.000525442,0.002092228,0.000000000],[0.227358206,0.000525442,0.000525442,0.001662399,0.000000000],[0.282328755,0.002403502,0.002606074,0.002449536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U24 - A30 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A12
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U17
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
Insertion    | Location [6] | 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 7, position 6 in cluster node
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 [12] | Right Index [11] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | Norm Constant [1.000000000000000] // Hairpin node U20:U20
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U20
