| 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 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_88225.1_Instance_1 HL_88225.1_HL_5WWT_001_C13_G22 | C | A | G | G | GGU | A | G | |||||||||||
| HL_88225.1_Sequence_1 HL_88225.1_HL_5WWT_001_C13_G22 | C | A | G | G | GGU | A | G | true | 94 | 0 | 0 | 0.85 | ||||||
| HL_88225.1_Instance_2 HL_88225.1_HL_3FOZ_004_C13_G22 | C | A | G | U | CGGU | A | G | |||||||||||
| HL_88225.1_Sequence_2 HL_88225.1_HL_3FOZ_004_C13_G22 | C | A | G | U | CGGU | A | G | true | 84 | 0 | 0 | 2.36 | ||||||
| HL_88225.1_Instance_3 HL_88225.1_HL_3TUP_001_C13_G22 | C | A | G | U | UGGU | A | G | |||||||||||
| HL_88225.1_Sequence_3 HL_88225.1_HL_3TUP_001_C13_G22 | C | A | G | U | UGGU | A | G | true | 88 | 0 | 0 | 1.75 | ||||||
| HL_88225.1_Instance_4 HL_88225.1_HL_3EPH_001_C13_G22 | C | A | G | U | GGU | A | G | |||||||||||
| HL_88225.1_Sequence_4 HL_88225.1_HL_3EPH_001_C13_G22 | C | A | G | U | GGU | A | G | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_88225.1_Instance_5 HL_88225.1_HL_1GAX_004_C913_G921 | C | A | G | C | GGA | A | G | |||||||||||
| HL_88225.1_Sequence_5 HL_88225.1_HL_1GAX_004_C913_G921 | C | A | G | C | GGA | A | G | true | 91 | 0 | 0 | 1.29 | ||||||
| HL_88225.1_Instance_6 HL_88225.1_HL_3AMU_001_U13_G22 | U | A | G | C | CAGGUC | A | G | |||||||||||
| HL_88225.1_Sequence_6 HL_88225.1_HL_3AMU_001_U13_G22 | U | A | G | C | CAGGUC | A | G | true | 42 | 0 | 0 | 8.65 |
1 6 cWW 2 3 s35 2 5 cWS 2 6 s55 3 4 s35JAR3D SCFG/MRF model for HL_88225.1:
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 C13 - G22 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009450884,0.015956080,0.011081266,0.165384558,0.000000000],[0.064779646,0.012271176,0.221537108,0.013630044,0.000000000],[0.011230126,0.168795395,0.002205978,0.021170298,0.000000000],[0.175296480,0.013008887,0.083924597,0.010277478,0.000000000],[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 C13 - G22 cWW BasepairNode | Deletion Probability [0.0000000000000372] | Pair Probability [[0.268206884,0.194638134,0.205690910,0.198820544,0.000000000],[0.015551543,0.012684090,0.002116031,0.012872646,0.000000000],[0.021028290,0.002116031,0.026951427,0.010065478,0.000000000],[0.007554325,0.007968863,0.006306246,0.007428559,0.000000000],[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 [0.000000000,0.000000000,0.004096682,0.494332924,0.331831217,0.004301516,0.164003824,0.001365561,0.000068278] | Right Letter Distribution [0.100000000,0.140000000,0.500000000,0.260000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair A14 - A21 cWS HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G15:G16 Interaction | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.812500000,0.000000000,0.000000000],[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 G15 Interaction | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[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 G16Sequences of instances from HL_88225.1:
> HL_88225.1 HL_5WWT_001 C 13 G 22 CAGGGGUAG > HL_88225.1 HL_3FOZ_004 C 13 G 22 CAGUCGGUAG > HL_88225.1 HL_3TUP_001 C 13 G 22 CAGUUGGUAG > HL_88225.1 HL_3EPH_001 C 13 G 22 CAGUGGUAG > HL_88225.1 HL_1GAX_004 C 913 G 921 CAGCGGAAG > HL_88225.1 HL_3AMU_001 U 13 G 22 UAGCCAGGUCAG