| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 3 I | 6 4 3 | 7 4 I | 8 5 4 | 9 5 I | 10 5 5 | 11 4 I | 12 4 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_73793.2_Instance_1 HL_73793.2_HL_5T83_003_G77_C85 | G | A | U | A | A | A | A | G | C | |||||||||||||
| HL_73793.2_Sequence_1 HL_73793.2_HL_5T83_003_G77_C85 | G | A | U | A | A | A | A | G | C | true | 96 | 0 | 0 | 0.51 | ||||||||
| HL_73793.2_Instance_2 HL_73793.2_HL_6DLR_003_G82_C90 | G | A | U | A | G | A | A | G | C | |||||||||||||
| HL_73793.2_Sequence_2 HL_73793.2_HL_6DLR_003_G82_C90 | G | A | U | A | G | A | A | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_73793.2_Instance_3 HL_73793.2_HL_6UFH_003_G70_C77 | G | G | U | U | G | G | C | C | ||||||||||||||
| HL_73793.2_Sequence_3 HL_73793.2_HL_6UFH_003_G70_C77 | G | G | U | U | G | G | C | C | true | 66 | 0 | 0 | 4.59 | |||||||||
| HL_73793.2_Instance_4 HL_73793.2_HL_5TBW_037_G1680_U1688 | G | U | U | A | U | C | U | U | U | |||||||||||||
| HL_73793.2_Sequence_4 HL_73793.2_HL_5TBW_037_G_1680_U_1688 | G | U | U | A | U | C | U | U | U | true | 62 | 0 | 0 | 5.11 |
1 2 s35 1 8 cWW 2 3 s35 2 7 tWH 3 5 s33 3 6 tWH 4 5 s35 5 6 s35 6 7 s35 7 8 s35JAR3D SCFG/MRF model for HL_73793.2:
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 [8] // Initial node G77 - C85 from junction BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.011043683,0.087705864,0.011663765,0.168825951,0.000000000],[0.015941238,0.010156843,0.158274510,0.013303388,0.000000000],[0.011498012,0.192719706,0.002332326,0.108853206,0.000000000],[0.155160397,0.013999784,0.020787547,0.017733780,0.000000000],[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 [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G77 - C85 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.341615830,0.003223851,0.284401550,0.003223851,0.000000000],[0.027594241,0.013680883,0.003223851,0.003223851,0.000000000],[0.003223851,0.061307595,0.118500437,0.034507085,0.000000000],[0.014567679,0.003223851,0.015451914,0.069029682,0.000000000],[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 [2] | Right Index [7] // Basepair A78 - A83 tWH BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.016740489,0.003704697,0.017387738,0.003704697,0.000000000],[0.037255609,0.298527778,0.003704697,0.003704697,0.000000000],[0.003704697,0.008880403,0.028173908,0.016477216,0.000000000],[0.389700464,0.057026375,0.074815886,0.036490649,0.000000000],[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 [3] | Right Index [6] // Basepair U79 - A82 tWH HairpinNode | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A80:A81 Interaction | Interacting Bases [1,1] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A80 Interaction | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A81Sequences of instances from HL_73793.2:
> HL_73793.2 HL_5T83_003 G 77 C 85 GAUAAAAGC > HL_73793.2 HL_6DLR_003 G 82 C 90 GAUAGAAGC > HL_73793.2 HL_6UFH_003 G 70 C 77 GGUUGGCC > HL_73793.2 HL_5TBW_037 G 1680 U 1688 GUUAUCUUU