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 [12] // Initial node C31 - G21 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000001549484556559301900000000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.094806833173160] // Cluster node C31:A36 and G19:G21
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.081378496,0.098546092,0.388749317,0.053999063,0.000000000],[0.063189619,0.045680214,0.002558985,0.039956944,0.000000000],[0.000713427,0.000588948,0.012712851,0.000457180,0.000000000],[0.004459938,0.000588948,0.205962796,0.000457180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A36 - G19 tHS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.165813762,0.027446076,0.026469528,0.026092728,0.000000000],[0.033494723,0.007176489,0.007176489,0.007176489,0.000000000],[0.456888233,0.071193943,0.071937937,0.015714203,0.000000000],[0.061889933,0.007176489,0.007176489,0.007176489,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G32 - A20 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.167477241,0.036008291,0.000377768,0.001878311,0.000000000],[0.168744503,0.032054522,0.000377768,0.000377768,0.000000000],[0.356845819,0.000377768,0.001929297,0.029052875,0.000000000],[0.170826576,0.032915957,0.000377768,0.000377768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G35 - A20 tSH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.008479529,0.014561897,0.009826657,0.149620471,0.000000000],[0.038597518,0.007703173,0.302258354,0.011499664,0.000000000],[0.009933633,0.176224842,0.001882503,0.019390841,0.000000000],[0.167564853,0.011015113,0.062328090,0.009112862,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C31 - G21 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.161548555,0.169966367,0.372406758,0.139858546,0.000000000],[0.001593759,0.001593759,0.001593759,0.001593759,0.000000000],[0.008609318,0.009842421,0.014904474,0.110113490,0.000000000],[0.001593759,0.001593759,0.001593759,0.001593759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A36 - G21 tSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.020000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.180000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A33
Insertion    | Location [3] | Length Distribution [0.002070169,0.952371991,0.045355528,0.000197607,0.000004705] | Letter Distribution [0.173076923,0.250000000,0.173076923,0.403846154,0.000000000]// Insertion after nucleotide 3, position 3 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 [0.824177637,0.131879734,0.000466622,0.043377026,0.000094267,0.000004713] | Right Letter Distribution [0.312500000,0.062500000,0.187500000,0.437500000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.047811319,0.050466058,0.302105938,0.047561334,0.000000000],[0.090847252,0.086472653,0.002900073,0.043001204,0.000000000],[0.000629921,0.000629921,0.061099075,0.000629921,0.000000000],[0.021682211,0.000629921,0.229627575,0.013905624,0.000000000],[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 [6] | Right Index [9] // Basepair A37 - G18 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010420873,0.110403380,0.010827885,0.125139785,0.000000000],[0.025695383,0.008447915,0.159702672,0.011573885,0.000000000],[0.010744835,0.136352265,0.002255713,0.197636037,0.000000000],[0.123320488,0.011981439,0.038018641,0.017478805,0.000000000],[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 [7] | Right Index [8] // Basepair A38 - U17 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
