| 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 3 I | 12 3 6 | 13 3 I | 14 3 7 | 15 3 I | 16 3 8 | 17 3 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_99867.1_Instance_1 HL_99867.1,HL_387D_001,G4_C13 | G | A | A | G | U | G | C | A | A | C | ||||||||||||||||
| HL_99867.1_Sequence_1 HL_99867.1387D_G4_C13 | G | A | A | G | U | G | C | A | A | C | true | 86 | 0 | 0 | 1.95 | |||||||||||
| HL_99867.1_Instance_2 HL_99867.1,HL_3PDR_003,G127_C136 | G | A | U | G | C | U | U | G | U | C | ||||||||||||||||
| HL_99867.1_Sequence_2 HL_99867.13PDR_G127_C136 | G | A | U | G | C | U | U | G | U | C | true | 94 | 0 | 0 | 0.85 | |||||||||||
| HL_99867.1_Instance_3 HL_99867.1,HL_3B31_001,A6184_U6193 | A | U | U | A | G | G | U | A | G | U | ||||||||||||||||
| HL_99867.1_Sequence_3 HL_99867.13B31_A_6184_U_6193 | A | U | U | A | G | G | U | A | G | U | true | 93 | 0 | 0 | 1.00 | |||||||||||
| HL_99867.1_Instance_4 HL_99867.1,HL_6XKO_003,G63_C72 | G | C | U | G | G | C | G | G | U | C | ||||||||||||||||
| HL_99867.1_Sequence_4 HL_99867.16XKO_G63_C72 | G | C | U | G | G | C | G | G | U | C | true | 96 | 0 | 0 | 0.51 | |||||||||||
| HL_99867.1_Instance_5 HL_99867.1,HL_4L47_036,G31_C39 | G | U | U | C | G | G | G | G | A | C | ||||||||||||||||
| HL_99867.1_Sequence_5 HL_99867.14L47_G31_C39 | G | U | U | C | G | G | G | G | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 10 cWW 2 3 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for HL_99867.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009368009,0.020030415,0.010540131,0.205635456,0.000000000],[0.016690726,0.009279029,0.195504376,0.012336141,0.000000000],[0.010440720,0.238674882,0.002020236,0.031139040,0.000000000],[0.192537250,0.012857479,0.022703477,0.010242632,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G4 - C13 cWW HairpinNode | Num Bases [8] | Left Index [2] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node A5:A12 Interaction | Interacting Bases [1,1] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A5 Interaction | Interacting Bases [2,2] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.642857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A6 Interaction | Interacting Bases [3,3] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G7 Interaction | Interacting Bases [4,4] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U8 Interaction | Interacting Bases [5,5] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G9 Interaction | Interacting Bases [6,6] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.357142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C10 Interaction | Interacting Bases [7,7] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A11 Interaction | Interacting Bases [8,8] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A12Sequences of instances from HL_99867.1:
> HL_99867.1 387D G 4 C 13 GAAGUGCAAC > HL_99867.1 3PDR G 127 C 136 GAUGCUUGUC > HL_99867.1 3B31 A 6184 U 6193 AUUAGGUAGU > HL_99867.1 6XKO G 63 C 72 GCUGGCGGUC > HL_99867.1 4L47 G 31 C 39 GUUCGGGGAC