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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G51 - C63 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [11] // Fixed node on left for 4MGN|1|A|G|52
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [3] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.326086957,0.021739130,0.630434783,0.021739130,0.000000000] | Position [1] | Left Index [3] | Right Index [11] // Fixed node on left for 4MGN|1|A|G|53
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Position [1] | Left Index [4] | Right Index [11] // Fixed node on left for 4MGN|1|A|C|54
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [5] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [5] | Right Index [11] // Fixed node on left for 4MGN|1|A|G|55
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [6] | Right Index [11] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [6] | Right Index [11] | Norm Constant [1.000000000000000] // Cluster node 4MGN|1|A|G|56:4MGN|1|A|U|57 and 4MGN|1|A|A|61:4MGN|1|A|A|61
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4MGN|1|A|U|57 - 4MGN|1|A|A|61 tWH 
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4MGN|1|A|G|56
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [10] // New Initial node after Cluster
HairpinNode  | Num Bases [3] | Left Index [8] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node G58:G60
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G58
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G59
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G60
