| 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 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_94352.4_Instance_1 HL_94352.4_HL_5XUZ_001_C-12_G-6 | C | U | A | A | G | U | G | |||||||||
| HL_94352.4_Sequence_1 HL_94352.4_HL_5XUZ_001_C-12_G-6 | C | U | A | A | G | U | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_94352.4_Instance_2 HL_94352.4_HL_5ID6_001_C11_G17 | C | U | A | A | G | U | G | |||||||||
| HL_94352.4_Sequence_2 HL_94352.4_HL_5ID6_001_C11_G17 | C | U | A | A | G | U | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_94352.4_Instance_3 HL_94352.4_HL_4V9F_003_G118_C122 | G | A | A | U | C | |||||||||||
| HL_94352.4_Sequence_3 HL_94352.4_HL_4V9F_003_G118_C122 | G | A | A | U | C | true | 85 | 0 | 0 | 1.47 |
1 2 s35 1 5 cWW 2 5 s55JAR3D SCFG/MRF model for HL_94352.4:
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 C-12 - G-6 from junction BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[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 [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair C-12 - G-6 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U-11:G-8 Interaction | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U-11 Interaction | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[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 A-9 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],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G-8 Insertion | Location [1] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_94352.4:
> HL_94352.4 HL_5XUZ_001 C -12 G -6 CUAAGUG > HL_94352.4 HL_5ID6_001 C 11 G 17 CUAAGUG > HL_94352.4 HL_4V9F_003 G 118 C 122 GAAUC