| 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 3 I | 10 3 5 | 11 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_29487.1_Instance_1 HL_29487.1_HL_2QUS_002_C32_G37 | C | U | G | A | U | G | ||||||||||||
| HL_29487.1_Sequence_1 HL_29487.1_HL_2QUS_002_C32_G37 | C | U | G | A | U | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_29487.1_Instance_2 HL_29487.1_HL_2QUW_002_C32_G37 | C | U | G | A | U | G | ||||||||||||
| HL_29487.1_Sequence_2 HL_29487.1_HL_2QUW_002_C32_G37 | C | U | G | A | U | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_29487.1_Instance_3 HL_29487.1_HL_5DH6_001_C16_G21 | C | U | G | A | U | G | ||||||||||||
| HL_29487.1_Sequence_3 HL_29487.1_HL_5DH6_001_C16_G21 | C | U | G | A | U | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_29487.1_Instance_4 HL_29487.1_HL_2OEU_001_C15_G20 | C | U | G | A | U | G | ||||||||||||
| HL_29487.1_Sequence_4 HL_29487.1_HL_2OEU_001_C15_G20 | C | U | G | A | U | G | true | 100 | 0 | 0 | 0.00 |
1 2 perp 1 5 s35 1 6 cWW 3 4 s35 4 6 perp 5 6 s55 2 5 6BPhJAR3D SCFG/MRF model for HL_29487.1:
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 [6] // Initial node C32 - G37 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 [6] // Basepair C32 - G37 cWW HairpinNode | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U33:U36 Interaction | Interacting Bases [1,1] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.016666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.016666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.950000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33 Interaction | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[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 G34 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 A35 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 U36Sequences of instances from HL_29487.1:
> HL_29487.1 HL_2QUS_002 C 32 G 37 CUGAUG > HL_29487.1 HL_2QUW_002 C 32 G 37 CUGAUG > HL_29487.1 HL_5DH6_001 C 16 G 21 CUGAUG > HL_29487.1 HL_2OEU_001 C 15 G 20 CUGAUG