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 [7] // Initial node G1255 - C1282 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000048001338920902248000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [1] | Right Index [7] | Norm Constant [0.005026101735550] // Cluster node G1255:G1258 and C1277:C1282
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.011163085,0.013192132,0.019946651,0.012972929,0.000000000],[0.002518887,0.002518887,0.002518887,0.002518887,0.000000000],[0.225176551,0.309004776,0.251654705,0.136738074,0.000000000],[0.002518887,0.002518887,0.002518887,0.002518887,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1255 - C1277 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010041880,0.019391351,0.011641525,0.191240548,0.000000000],[0.018213986,0.008378062,0.218250356,0.013353236,0.000000000],[0.011592485,0.230126887,0.002128781,0.026054525,0.000000000],[0.190871828,0.013570829,0.024804352,0.010339370,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1258 - C1277 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1255 - C1282 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.045718505,0.071211636,0.067574328,0.059346113,0.000000000],[0.067020919,0.068682141,0.068754223,0.066310020,0.000000000],[0.033617316,0.060370142,0.102093763,0.067927601,0.000000000],[0.066643012,0.022123010,0.068785007,0.063822266,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1255 - G1258 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1256
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U1278
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1279
Insertion    | Location [2] | Length Distribution [0.010744024,0.644641418,0.010744024,0.005909213,0.322320709,0.005372012,0.000268601] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [6] | Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000]// Insertion after nucleotide 6, position 6 in cluster node
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 [4] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
