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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[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 [13] // Basepair U1479 - A1874 cWW 
ClusterNode  | Deletion Probability [0.000000000000015254027177953870338373321144532320374926368314] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [12] | Norm Constant [0.312390441543080] // Cluster node 5TBW|1|1|G|1480:5TBW|1|1|G|1483 and 5TBW|1|1|C|1872:5TBW|1|1|U|1873
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.031021441,0.372326222,0.003624252,0.036446633,0.000000000],[0.003624252,0.026405017,0.012653299,0.003624252,0.000000000],[0.103678615,0.003624252,0.032591280,0.016294714,0.000000000],[0.003624252,0.003624252,0.033407624,0.313429642,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5TBW|1|1|A|1481 - 5TBW|1|1|C|1872 tHW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.013854278,0.017490019,0.000634771,0.003852439,0.000000000],[0.008036166,0.007901960,0.000634771,0.000634771,0.000000000],[0.377138465,0.004443394,0.031837578,0.454240370,0.000000000],[0.052697754,0.025333725,0.000634771,0.000634771,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5TBW|1|1|G|1480 - 5TBW|1|1|U|1873 tSH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.017035113,0.277461015,0.003022606,0.242124836,0.000000000],[0.013660292,0.014465734,0.009818556,0.014612890,0.000000000],[0.003022606,0.012736220,0.014938620,0.312161581,0.000000000],[0.014900712,0.014057333,0.013985305,0.021996583,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5TBW|1|1|G|1483 - 5TBW|1|1|U|1873 tWW 
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 3, position 2 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 [5] | Right Index [10] // Initial node 5TBW|1|1|U|1484 - 5TBW|1|1|U|1871 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 5TBW|1|1|G|1483
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [6] | Right Index [10] // Junction node G1485 - U1871 ID J7537
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Basepair G1485 - C1857 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [8] | Right Index [10] // Initial node 5TBW|1|1|A|1858 - 5TBW|1|1|U|1871 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 5TBW|1|1|C|1857
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.026235093,0.062205457,0.028019647,0.586764415,0.000000000],[0.007072752,0.003867915,0.078392192,0.004182258,0.000000000],[0.003995015,0.079408468,0.000824091,0.021484428,0.000000000],[0.079142195,0.004452488,0.009291068,0.004662519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair A1859 - U1871 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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
