Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [10] // Initial node C33 - G50 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004717578,0.008091894,0.027414702,0.090485831,0.000000000],[0.009770034,0.004029345,0.562172037,0.006549320,0.000000000],[0.005552839,0.098023820,0.005055683,0.011187614,0.000000000],[0.091011380,0.006239176,0.064847658,0.004851089,0.000000000],[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 [0.416274113910334] // Cluster node A34:G37 and A49:A49
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.528849073,0.083541625,0.076461802,0.077107477,0.000000000],[0.005827225,0.001165445,0.001165445,0.001165445,0.000000000],[0.153166296,0.026129033,0.026624910,0.009472662,0.000000000],[0.005827225,0.001165445,0.001165445,0.001165445,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A34 - A49 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.071085104,0.082858788,0.000856485,0.004078472,0.000000000],[0.071717548,0.075170449,0.000856485,0.000856485,0.000000000],[0.311861171,0.002552574,0.012366685,0.212322902,0.000000000],[0.077266991,0.074436891,0.000856485,0.000856485,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G37 - A49 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 A35
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 [[0.052788444,0.053258103,0.374620487,0.057379170,0.000000000],[0.061531689,0.055822259,0.003180167,0.055277512,0.000000000],[0.000636033,0.000636033,0.015407242,0.000636033,0.000000000],[0.003028710,0.000636033,0.264526051,0.000636033,0.000000000],[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 [[0.012844072,0.159282715,0.013171233,0.114580161,0.000000000],[0.015240908,0.009601556,0.118644620,0.013806282,0.000000000],[0.012933937,0.153035139,0.002695858,0.207733360,0.000000000],[0.110794989,0.014924503,0.018737671,0.021972996,0.000000000],[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
