| 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 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_50537.2_Instance_1 HL_50537.2_HL_4WJ4_002_A31_U39 | A | C | U | G | U | U | A | A | U | |||||||||||||
| HL_50537.2_Sequence_1 HL_50537.2_HL_4WJ4_002_A31_U39 | A | C | U | G | U | U | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_50537.2_Instance_2 HL_50537.2_HL_4WJ4_005_A31_U39 | A | C | U | G | U | U | A | A | U | |||||||||||||
| HL_50537.2_Sequence_2 HL_50537.2_HL_4WJ4_005_A31_U39 | A | C | U | G | U | U | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_50537.2_Instance_3 HL_50537.2_HL_3KFU_005_G31_C39 | G | C | U | G | U | U | A | A | C | |||||||||||||
| HL_50537.2_Sequence_3 HL_50537.2_HL_3KFU_005_G31_C39 | G | C | U | G | U | U | A | A | C | true | 100 | 0 | 0 | 0.06 |
1 2 s35 1 8 cWW 2 7 bif 4 5 perp 5 6 s35 7 8 s35JAR3D SCFG/MRF model for HL_50537.2:
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 A31 - U39 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009341597,0.021222893,0.010204228,0.220628516,0.000000000],[0.017209227,0.009475562,0.195205747,0.011223855,0.000000000],[0.010150854,0.208524333,0.002037222,0.043966533,0.000000000],[0.195018545,0.011831944,0.022937162,0.011021781,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair A31 - U39 cWW BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.026873761,0.030189235,0.006557195,0.006557195,0.000000000],[0.731077818,0.076793656,0.006557195,0.006557195,0.000000000],[0.006557195,0.006557195,0.027515142,0.041978435,0.000000000],[0.006557195,0.006557195,0.006557195,0.006557195,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair C32 - A38 bif HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U33:U36 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33 Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G34 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U35 Interaction | Interacting Bases [4,4] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U36Sequences of instances from HL_50537.2:
> HL_50537.2 HL_4WJ4_002 A 31 U 39 ACUGUUAAU > HL_50537.2 HL_4WJ4_005 A 31 U 39 ACUGUUAAU > HL_50537.2 HL_3KFU_005 G 31 C 39 GCUGUUAAC