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 [22] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 G5 - C35 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.408702443,0.030010298,0.003890946,0.018600071,0.000000000],[0.029232420,0.014184148,0.011587973,0.014194456,0.000000000],[0.003890946,0.011604643,0.359806718,0.021928993,0.000000000],[0.018577888,0.014190992,0.021454432,0.018142633,0.000000000],[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 [21] // Basepair A6 - A34 tWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [20] // Fixed node on left for 6SY6|1|D|G|7
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [20] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.381184813,0.003615770,0.318975856,0.003615770,0.000000000],[0.030948835,0.015344049,0.003615770,0.003615770,0.000000000],[0.003615770,0.008956754,0.132906372,0.038702064,0.000000000],[0.016338652,0.003615770,0.017330382,0.017617604,0.000000000],[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 [4] | Right Index [20] // Basepair A8 - A33 tWH 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000150677338694597876100351] | Num Left Bases [8] | Num Right Bases [7] | Left Index [5] | Right Index [19] | Norm Constant [0.000040477505943] // Cluster node 6SY6|1|D|A|9:6SY6|1|D|G|17 and 6SY6|1|D|C|26:6SY6|1|D|A|32
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|17 - 6SY6|1|D|C|26 cWW 
Interaction  | Interacting Bases [7,10] | 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]] // Cluster Interaction 6SY6|1|D|G|16 - 6SY6|1|D|A|27 cWW 
Interaction  | Interacting Bases [3,11] | Pair Probability [[0.020814325,0.017422103,0.019901827,0.012513985,0.000000000],[0.002436905,0.002436905,0.214331865,0.002436905,0.000000000],[0.236896108,0.002436905,0.263298345,0.195326202,0.000000000],[0.002436905,0.002436905,0.002436905,0.002436905,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|11 - 6SY6|1|D|G|28 tSS 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.284046767,0.205222254,0.002992204,0.002992204,0.000000000],[0.012555813,0.008788211,0.002992204,0.002992204,0.000000000],[0.002992204,0.002992204,0.318828243,0.140636672,0.000000000],[0.002992204,0.002992204,0.002992204,0.002992204,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|16 - 6SY6|1|D|G|28 bif 
Interaction  | Interacting Bases [2,14] | 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 6SY6|1|D|U|10 - 6SY6|1|D|A|31 tWH 
Interaction  | Interacting Bases [1,15] | Pair Probability [[0.381184813,0.003615770,0.318975856,0.003615770,0.000000000],[0.030948835,0.015344049,0.003615770,0.003615770,0.000000000],[0.003615770,0.008956754,0.132906372,0.038702064,0.000000000],[0.016338652,0.003615770,0.017330382,0.017617604,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|A|9 - 6SY6|1|D|A|32 tWH 
Interaction  | Interacting Bases [8,15] | Pair Probability [[0.021432702,0.017618490,0.020295984,0.012884448,0.000000000],[0.002588469,0.002588469,0.225207716,0.002588469,0.000000000],[0.278454716,0.002588469,0.251629900,0.151768294,0.000000000],[0.002588469,0.002588469,0.002588469,0.002588469,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|G|17 - 6SY6|1|D|A|32 tSS 
Interaction  | Interacting Bases [10,14] | Pair Probability [[0.105678172,0.077024050,0.079578597,0.075017401,0.000000000],[0.082314407,0.082309394,0.003542979,0.052346388,0.000000000],[0.079619001,0.003607345,0.006695471,0.042552099,0.000000000],[0.078700115,0.073784465,0.078299920,0.078930195,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|A|27 - 6SY6|1|D|A|31 cSS 
Interaction  | Interacting Bases [9,15] | Pair Probability [[0.074223484,0.073792369,0.071881206,0.074519741,0.000000000],[0.102548686,0.075294337,0.003500217,0.067006249,0.000000000],[0.078701774,0.003446523,0.006762627,0.080050254,0.000000000],[0.074996893,0.072309095,0.071887647,0.069078898,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6SY6|1|D|C|26 - 6SY6|1|D|A|32 cSS 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.906250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6SY6|1|D|U|12
Interaction  | Interacting Bases [5,5] | 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 6SY6|1|D|U|13
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.971153846,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009615385,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009615385,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009615385,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6SY6|1|D|A|14
Interaction  | Interacting Bases [12,12] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 6SY6|1|D|A|29
Interaction  | Interacting Bases [13,13] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.875000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 6SY6|1|D|G|30
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 10, position 6 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 [13] | Right Index [12] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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
