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 [18] // Initial node G487 - C515 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000145428340716098440000000] | Num Left Bases [3] | Num Right Bases [11] | Left Index [1] | Right Index [18] | Norm Constant [0.005052243386544] // Cluster node G487:A489 and G503:C515
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.018317703,0.016794378,0.044113215,0.014232773,0.000000000],[0.017764530,0.015600448,0.344421436,0.017561692,0.000000000],[0.015465936,0.015129057,0.019364047,0.011146893,0.000000000],[0.019374661,0.016135933,0.401553078,0.013024218,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U488 - G503 cSW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.113009038,0.114014480,0.146062469,0.122836824,0.000000000],[0.131726501,0.119503802,0.001361615,0.118337612,0.000000000],[0.001361615,0.001361615,0.006596738,0.001361615,0.000000000],[0.006483836,0.001361615,0.113259011,0.001361615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A489 - G503 tHS 
Interaction  | Interacting Bases [1,12] | Pair Probability [[0.011418641,0.014331648,0.024329846,0.014025501,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.224007246,0.230872701,0.259048862,0.202033724,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G487 - G512 tSS 
Interaction  | Interacting Bases [2,13] | Pair Probability [[0.029444578,0.002831562,0.002889484,0.003092144,0.000000000],[0.019081002,0.000684518,0.003470025,0.003413354,0.000000000],[0.402422274,0.002994065,0.001328282,0.000684518,0.000000000],[0.489063609,0.037231547,0.000684518,0.000684518,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U488 - A513 tHH 
Interaction  | Interacting Bases [1,14] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G487 - C515 cWW 
Interaction  | Interacting Bases [6,10] | Pair Probability [[0.020051501,0.002539818,0.142297221,0.002539818,0.000000000],[0.263882817,0.012018367,0.235478309,0.002539818,0.000000000],[0.002539818,0.002539818,0.017348636,0.026230988,0.000000000],[0.025227938,0.002539818,0.012157548,0.230067766,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C505 - A509 tWH 
Interaction  | Interacting Bases [7,11] | Pair Probability [[0.113009038,0.131726501,0.001361615,0.006483836,0.000000000],[0.114014480,0.119503802,0.001361615,0.001361615,0.000000000],[0.146062469,0.001361615,0.006596738,0.113259011,0.000000000],[0.122836824,0.118337612,0.001361615,0.001361615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G506 - A511 tSH 
Interaction  | Interacting Bases [5,12] | Pair Probability [[0.033845764,0.260862878,0.004239511,0.004239511,0.000000000],[0.016079117,0.013703666,0.004239511,0.004239511,0.000000000],[0.004239511,0.004239511,0.433852082,0.199261383,0.000000000],[0.004239511,0.004239511,0.004239511,0.004239511,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G504 - G512 bif 
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A507
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A508
Insertion    | Location [10] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 14, position 10 in cluster node
Insertion    | Location [13] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 17, position 13 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.012225429,0.015145471,0.014725930,0.034760566,0.000000000],[0.381707213,0.018478793,0.035925510,0.016513221,0.000000000],[0.015080020,0.029754800,0.003718062,0.015583401,0.000000000],[0.042294737,0.014884503,0.334044557,0.015157789,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair C490 - A502 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[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 [5] | Right Index [6] // Basepair C491 - G501 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
