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 [0.0000244705618206] | Pair Probability [[0.009303158,0.018489895,0.010627125,0.192911785,0.000000000],[0.017471954,0.009238523,0.216141290,0.012945225,0.000000000],[0.010587651,0.236901681,0.002010592,0.024697007,0.000000000],[0.192085542,0.013106691,0.023637380,0.009844500,0.000000000],[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 [12] // Basepair G1515 - C1520 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.083928127,0.092947454,0.001687479,0.009202510,0.000000000],[0.103889074,0.078873753,0.001687479,0.001687479,0.000000000],[0.183115013,0.001687479,0.010347045,0.176029550,0.000000000],[0.147730183,0.103812416,0.001687479,0.001687479,0.000000000],[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 [11] // Basepair G1516 - A1519 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.103324974,0.109383411,0.001240347,0.005845761,0.000000000],[0.104092605,0.109130123,0.001240347,0.001240347,0.000000000],[0.225562147,0.001240347,0.006063665,0.105276001,0.000000000],[0.115338265,0.108540964,0.001240347,0.001240347,0.000000000],[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 [3] | Right Index [10] // Basepair G1517 - A1518 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.103324974,0.104092605,0.193666370,0.115338265,0.000000000],[0.109383411,0.109130123,0.001240347,0.108540964,0.000000000],[0.033136125,0.001240347,0.006063665,0.001240347,0.000000000],[0.005845761,0.001240347,0.105276001,0.001240347,0.000000000],[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 [4] | Right Index [9] // Basepair A1518 - G1517 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.089420779,0.082779780,0.191033087,0.145754852,0.000000000],[0.098147433,0.086140462,0.001651418,0.107235222,0.000000000],[0.001651418,0.001651418,0.009856129,0.001651418,0.000000000],[0.008845142,0.001651418,0.170878606,0.001651418,0.000000000],[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 A1519 - G1516 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010250831,0.062344241,0.011126372,0.173783681,0.000000000],[0.017440548,0.009785795,0.199811270,0.013206254,0.000000000],[0.011096934,0.190253136,0.002195921,0.081342052,0.000000000],[0.166498348,0.013338697,0.022714799,0.014811119,0.000000000],[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 C1520 - G1515 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
