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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009067845,0.019603119,0.010071826,0.220747538,0.000000000],[0.016903319,0.009136162,0.200075347,0.011537189,0.000000000],[0.010030419,0.221402449,0.001972052,0.035870644,0.000000000],[0.188702726,0.011947758,0.022632251,0.010299353,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair A42 - U31 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.116080178,0.176285660,0.146810382,0.024758432,0.000000000],[0.013168086,0.010233170,0.021665544,0.023830889,0.000000000],[0.143331769,0.023806144,0.003457474,0.137030898,0.000000000],[0.021580629,0.024141361,0.014060792,0.099758592,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair A43 - C30 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [6] | Norm Constant [0.252410397920198] // Cluster node 7EL1|1|B|U|44:7EL1|1|B|U|46 and 7EL1|1|B|A|29:7EL1|1|B|A|29
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.008939441,0.017346894,0.010053653,0.189181225,0.000000000],[0.019185212,0.009261737,0.211381604,0.011886470,0.000000000],[0.010061557,0.210351303,0.001973383,0.023097129,0.000000000],[0.220529544,0.011612576,0.035454589,0.009683680,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EL1|1|B|U|46 - 7EL1|1|B|A|29 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.063569176,0.098738364,0.143590998,0.069048957,0.000000000],[0.059501789,0.068138337,0.001998079,0.029008056,0.000000000],[0.027691089,0.001998079,0.081238651,0.077145551,0.000000000],[0.064690024,0.083122071,0.001998079,0.128522701,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EL1|1|B|U|44 - 7EL1|1|B|U|46 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.388888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7EL1|1|B|C|45
InitialNode  | Left Length Distribution [0.992332775,0.007314709,0.000352516] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.992332775,0.007314709,0.000352516] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
