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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004553963,0.008166350,0.026176706,0.094927059,0.000000000],[0.009682505,0.004638079,0.555559699,0.006585388,0.000000000],[0.005294135,0.096972482,0.004989559,0.011205720,0.000000000],[0.096157693,0.006344894,0.063919821,0.004825947,0.000000000],[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 [10] // Basepair C33 - G50 cWW 
ClusterNode  | Deletion Probability [0.0000000000031115] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [9] | Norm Constant [0.365714344673504] // Cluster node 3SIV|1|C|A|34:3SIV|1|C|G|37 and 3SIV|1|F|A|49:3SIV|1|F|A|49
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.386660257,0.089930574,0.092289748,0.086312922,0.000000000],[0.004202078,0.001199031,0.033347911,0.001199031,0.000000000],[0.169868484,0.001199031,0.034534058,0.091457706,0.000000000],[0.004202078,0.001199031,0.001199031,0.001199031,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3SIV|1|C|A|34 - 3SIV|1|F|A|49 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.071386868,0.075572621,0.000856952,0.004038816,0.000000000],[0.071917221,0.075397625,0.000856952,0.000856952,0.000000000],[0.311431012,0.002548272,0.012457694,0.216287725,0.000000000],[0.079686809,0.074990577,0.000856952,0.000856952,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3SIV|1|C|G|37 - 3SIV|1|F|A|49 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.953125000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3SIV|1|C|A|35
Insertion    | Location [2] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
InitialNode  | 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 [5] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.052834690,0.053227214,0.373726391,0.058977624,0.000000000],[0.055932640,0.055803123,0.003171226,0.055501860,0.000000000],[0.000634245,0.000634245,0.015503117,0.000634245,0.000000000],[0.002989200,0.000634245,0.269161687,0.000634245,0.000000000],[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 [5] | Right Index [8] // Basepair A38 - G48 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012304240,0.152595251,0.012221578,0.137557369,0.000000000],[0.014828613,0.010745729,0.115211142,0.013322044,0.000000000],[0.012014775,0.148821138,0.002566200,0.197277540,0.000000000],[0.113221234,0.014204047,0.018215096,0.024894003,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [7] // Basepair G39 - U47 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
