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 [13] // Initial node C1147 - G1216 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000001940553474955695100000000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [13] | Norm Constant [0.000558380037188] // Cluster node C1147:A1152 and G1214:G1216
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.042875527,0.043256990,0.400078329,0.046604180,0.000000000],[0.049976915,0.045339634,0.003616168,0.044897183,0.000000000],[0.000516595,0.000516595,0.017519574,0.000516595,0.000000000],[0.002459961,0.000516595,0.300792562,0.000516595,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1152 - G1214 tHS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.107954545,0.054632867,0.054632867,0.054632867,0.000000000],[0.127185315,0.054632867,0.054632867,0.054632867,0.000000000],[0.054632867,0.054632867,0.054632867,0.054632867,0.000000000],[0.054632867,0.054632867,0.054632867,0.054632867,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1148 - A1215 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.185166390,0.043167026,0.000446204,0.002124765,0.000000000],[0.186813816,0.039161625,0.000446204,0.000446204,0.000000000],[0.261563424,0.000446204,0.002161764,0.037115194,0.000000000],[0.201269312,0.038779462,0.000446204,0.000446204,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1151 - A1215 tSH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.009613617,0.017593128,0.010983027,0.192350441,0.000000000],[0.021287894,0.008639455,0.234523700,0.012787711,0.000000000],[0.011096459,0.200570476,0.002109537,0.023296342,0.000000000],[0.204768830,0.012284769,0.027115440,0.010979173,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1147 - G1216 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.204273875,0.182392691,0.228460848,0.175009089,0.000000000],[0.001996147,0.001996147,0.001996147,0.001996147,0.000000000],[0.010954656,0.012643890,0.019492821,0.150802954,0.000000000],[0.001996147,0.001996147,0.001996147,0.001996147,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1152 - G1216 tSS 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.056456460,0.057489227,0.055785276,0.056733612,0.000000000],[0.136969236,0.057810615,0.007079764,0.053147720,0.000000000],[0.060169857,0.061092715,0.055484166,0.061453996,0.000000000],[0.111667921,0.056875119,0.054584017,0.057200297,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1147 - A1152 cSS 
Interaction  | Interacting Bases [7,8] | Pair Probability [[0.195141897,0.160173003,0.197628067,0.154493037,0.000000000],[0.029233204,0.029516469,0.003600697,0.030054980,0.000000000],[0.029730386,0.030050892,0.013725809,0.030122553,0.000000000],[0.029973668,0.007433790,0.028524377,0.030597170,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1215 - G1216 cSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.583333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U1149
Insertion    | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Initial node C1153 - C1213 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.018665872,0.615612422,0.004897383,0.004897383,0.000000000],[0.021553581,0.253036378,0.004897383,0.004897383,0.000000000],[0.004897383,0.004897383,0.018574216,0.004897383,0.000000000],[0.004897383,0.004897383,0.023583701,0.004897383,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair A1154 - C1213 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013091073,0.162345844,0.013424526,0.116783626,0.000000000],[0.015534003,0.009786201,0.120926247,0.014071788,0.000000000],[0.013182666,0.146362737,0.002747701,0.202112848,0.000000000],[0.112925662,0.015211513,0.019098011,0.022395553,0.000000000],[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 [8] | Right Index [9] // Basepair G1155 - C1212 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
