| 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 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_06569.1_Instance_1 HL_06569.1_HL_7A0S_007_A202_U207 | A | G | A | A | U | U | ||||||||||
| HL_06569.1_Sequence_1 HL_06569.1_HL_7A0S_007_A202_U207 | A | G | A | A | U | U | true | 100 | 0 | 0 | 0.00 | |||||
| HL_06569.1_Instance_2 HL_06569.1_HL_4Y4O_109_A225_U230 | A | G | A | A | A | U | ||||||||||
| HL_06569.1_Sequence_2 HL_06569.1_HL_4Y4O_109_A225_U230 | A | G | A | A | A | U | true | 95 | 0 | 0 | 0.51 | |||||
| HL_06569.1_Instance_3 HL_06569.1_HL_4C9D_002_C21_G25 | C | G | U | A | G | |||||||||||
| HL_06569.1_Sequence_3 HL_06569.1_HL_4C9D_002_C21_G25 | C | G | U | A | G | true | 91 | 0 | 0 | 0.88 | ||||||
| HL_06569.1_Instance_4 HL_06569.1_HL_5TBW_075_C108_G114 | C | A | C | A | U | U | G | |||||||||
| HL_06569.1_Sequence_4 HL_06569.1_HL_5TBW_075_C108_G114 | C | A | C | A | U | U | G | true | 63 | 0 | 0 | 3.48 |
1 2 s35 1 5 cWW 2 3 s35 2 4 tSH 3 4 s55 4 5 s35JAR3D SCFG/MRF model for HL_06569.1:
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 [5] // Initial node A202 - U207 from junction BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.009228795,0.019179884,0.010238170,0.216808949,0.000000000],[0.018533875,0.009460985,0.216925123,0.011842533,0.000000000],[0.010289084,0.196034129,0.002025733,0.037602685,0.000000000],[0.194873981,0.011923789,0.024413241,0.010619045,0.000000000],[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 [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair A202 - U207 cWW BasepairNode | Deletion Probability [0.0000060823043662] | Pair Probability [[0.107010574,0.113285114,0.001284591,0.046687034,0.000000000],[0.107805585,0.113022792,0.001284591,0.001284591,0.000000000],[0.157305214,0.001284591,0.006279955,0.109031193,0.000000000],[0.119452378,0.112412618,0.001284591,0.001284591,0.000000000],[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 [0.741082411,0.255227552,0.003536285,0.000153752] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [4] // Basepair G203 - A205 tSH HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A204:A204 Interaction | Interacting Bases [1,1] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A204Sequences of instances from HL_06569.1:
> HL_06569.1 HL_7A0S_007 A 202 U 207 AGAAUU > HL_06569.1 HL_4Y4O_109 A 225 U 230 AGAAAU > HL_06569.1 HL_4C9D_002 C 21 G 25 CGUAG > HL_06569.1 HL_5TBW_075 C 108 G 114 CACAUUG