| 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 3 3 | 7 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_62869.2_Instance_1 HL_62869.2_HL_4Y4O_105_G123_C128 | G | G | G | A | A | C | ||||||||||
| HL_62869.2_Sequence_1 HL_62869.2_HL_4Y4O_105_G123_C128 | G | G | G | A | A | C | true | 91 | 0 | 0 | 0.85 | |||||
| HL_62869.2_Instance_2 HL_62869.2_HL_5J7L_136_G123_C128 | G | G | A | A | A | C | ||||||||||
| HL_62869.2_Sequence_2 HL_62869.2_HL_5J7L_136_G123_C128 | G | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_62869.2_Instance_3 HL_62869.2_HL_7A0S_003_G121_C126 | G | G | A | A | A | C | ||||||||||
| HL_62869.2_Sequence_3 HL_62869.2_HL_7A0S_003_G121_C126 | G | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_62869.2_Instance_4 HL_62869.2_HL_4WF9_003_G122_C127 | G | G | A | A | A | C | ||||||||||
| HL_62869.2_Sequence_4 HL_62869.2_HL_4WF9_003_G122_C127 | G | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 5 cWW 2 5 s55 3 4 s35 2 3 6BRJAR3D SCFG/MRF model for HL_62869.2:
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 [5] // Initial node G123 - C128 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [1] | Right Index [5] // Basepair G123 - C128 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G124:A127 Interaction | Interacting Bases [1,1] | Pair Probability [[0.022727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.022727273,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.931818182,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.022727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G124 Interaction | Interacting Bases [2,2] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A126 Interaction | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A127 Insertion | Location [1] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_62869.2:
> HL_62869.2 HL_4Y4O_105 G 123 C 128 GGGAAC > HL_62869.2 HL_5J7L_136 G 123 C 128 GGAAAC > HL_62869.2 HL_7A0S_003 G 121 C 126 GGAAAC > HL_62869.2 HL_4WF9_003 G 122 C 127 GGAAAC