| 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 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 4 I | 16 4 8 | 17 4 I | 18 4 9 | 19 3 I | 20 3 10 | 21 2 I | 22 2 11 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_89082.1_Instance_1 HL_89082.1_HL_3EGZ_005_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | |||||||||||||||
| HL_89082.1_Sequence_1 HL_89082.1_HL_3EGZ_005_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_89082.1_Instance_2 HL_89082.1_HL_3EGZ_007_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | |||||||||||||||
| HL_89082.1_Sequence_2 HL_89082.1_HL_3EGZ_007_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_89082.1_Instance_3 HL_89082.1_HL_3EGZ_001_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | |||||||||||||||
| HL_89082.1_Sequence_3 HL_89082.1_HL_3EGZ_001_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_89082.1_Instance_4 HL_89082.1_HL_3EGZ_003_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | |||||||||||||||
| HL_89082.1_Sequence_4 HL_89082.1_HL_3EGZ_003_G12_C24 | G | A | A | G | A | A | U | A | C | G | A | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 11 cWW 2 3 s35 2 10 cWW 3 4 s35 4 5 s35 7 8 s35 9 10 s35 10 11 s35 8 7 7BPh 4 8 6BPhJAR3D SCFG/MRF model for HL_89082.1:
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 [11] // Initial node G12 - C24 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 [11] // Basepair G12 - C24 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.013555679,0.330164293,0.011831118,0.031455458,0.000000000],[0.011882468,0.011387993,0.023871313,0.011757050,0.000000000],[0.011553315,0.028303234,0.002917028,0.266930641,0.000000000],[0.025035369,0.012901190,0.012338114,0.194115737,0.000000000],[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 [10] // Basepair A13 - C23 cWW HairpinNode | Num Bases [7] | Left Index [3] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node A14:A22 Interaction | Interacting Bases [1,1] | 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 A14 Interaction | Interacting Bases [2,2] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.016666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.950000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15 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 A16 Interaction | Interacting Bases [4,4] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U18 Interaction | Interacting Bases [5,5] | 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 A19 Interaction | Interacting Bases [6,6] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.950000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.016666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C20 Interaction | Interacting Bases [7,7] | 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 A22 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 in Hairpin after nucleotide 5, position 3 Insertion | Location [6] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 8, position 6Sequences of instances from HL_89082.1:
> HL_89082.1 HL_3EGZ_005 G 12 C 24 GAAGAAUACGACC > HL_89082.1 HL_3EGZ_007 G 12 C 24 GAAGAAUACGACC > HL_89082.1 HL_3EGZ_001 G 12 C 24 GAAGAAUACGACC > HL_89082.1 HL_3EGZ_003 G 12 C 24 GAAGAAUACGACC