| 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_82678.2_Instance_1 HL_82678.2_HL_6D12_001_C309_G315 | C | A | U | G | U | G | G | |||||||||||
| HL_82678.2_Sequence_1 HL_82678.2_HL_6D12_001_C309_G315 | C | A | U | G | U | G | G | true | 88 | 0 | 0 | 1.15 | ||||||
| HL_82678.2_Instance_2 HL_82678.2_HL_6D12_002_C328_G334 | C | A | U | G | U | G | G | |||||||||||
| HL_82678.2_Sequence_2 HL_82678.2_HL_6D12_002_C328_G334 | C | A | U | G | U | G | G | true | 88 | 0 | 0 | 1.15 | ||||||
| HL_82678.2_Instance_3 HL_82678.2_HL_2Y9H_007_C11_G16 | C | G | C | G | U | G | ||||||||||||
| HL_82678.2_Sequence_3 HL_82678.2_HL_2Y9H_007_C11_G16 | C | G | C | G | U | G | true | 86 | 0 | 0 | 1.30 | |||||||
| HL_82678.2_Instance_4 HL_82678.2_HL_4V88_216_C1359_G1364 | C | A | U | U | U | G | ||||||||||||
| HL_82678.2_Sequence_4 HL_82678.2_HL_4V88_216_C_1359_G_1364 | C | A | U | U | U | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_82678.2_Instance_5 HL_82678.2_HL_2QUS_003_C42_G47 | C | G | U | G | A | G | ||||||||||||
| HL_82678.2_Sequence_5 HL_82678.2_HL_2QUS_003_C42_G47 | C | G | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_82678.2_Instance_6 HL_82678.2_HL_2QUW_003_C42_G47 | C | G | U | G | A | G | ||||||||||||
| HL_82678.2_Sequence_6 HL_82678.2_HL_2QUW_003_C42_G47 | C | G | U | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 6 cWW 2 3 s35 2 6 s55JAR3D SCFG/MRF model for HL_82678.2:
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 [6] // Initial node C309 - G315 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[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 [6] // Basepair C309 - G315 cWW HairpinNode | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A310:G314 Interaction | Interacting Bases [1,1] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A310 Interaction | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.687500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U311 Interaction | Interacting Bases [3,3] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U313 Interaction | Interacting Bases [4,4] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G314 Insertion | Location [2] | Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2Sequences of instances from HL_82678.2:
> HL_82678.2 HL_6D12_001 C 309 G 315 CAUGUGG > HL_82678.2 HL_6D12_002 C 328 G 334 CAUGUGG > HL_82678.2 HL_2Y9H_007 C 11 G 16 CGCGUG > HL_82678.2 HL_4V88_216 C 1359 G 1364 CAUUUG > HL_82678.2 HL_2QUS_003 C 42 G 47 CGUGAG > HL_82678.2 HL_2QUW_003 C 42 G 47 CGUGAG