| 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 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_48810.1_Instance_1 HL_48810.1_HL_4RDX_001_C13_G22 | C | A | G | CUG | G | U | U | A | G | |||||||||||
| HL_48810.1_Sequence_1 HL_48810.1_HL_4RDX_001_C13_G22 | C | A | G | CUG | G | U | U | A | G | true | 96 | 0 | 0 | 0.71 | ||||||
| HL_48810.1_Instance_2 HL_48810.1_HL_4RDX_004_C13_G22 | C | A | G | CUG | G | U | U | A | G | |||||||||||
| HL_48810.1_Sequence_2 HL_48810.1_HL_4RDX_004_C13_G22 | C | A | G | CUG | G | U | U | A | G | true | 96 | 0 | 0 | 0.71 | ||||||
| HL_48810.1_Instance_3 HL_48810.1_HL_3WQY_001_C1613_G1622 | C | A | G | C | G | G | G | A | G | |||||||||||
| HL_48810.1_Sequence_3 HL_48810.1_HL_3WQY_001_C_1613_G_1622 | C | A | G | C | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 7 cWW 2 3 s35 2 7 s55 4 5 s35 5 4 7BRJAR3D SCFG/MRF model for HL_48810.1:
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 [7] // Initial node C13 - G22 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C13 - G22 cWW HairpinNode | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [0.999999999999999] // Hairpin node A14:A21 Interaction | Interacting Bases [1,1] | 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 A14 Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G15 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],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G19 Interaction | Interacting Bases [4,4] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.323529412,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.617647059,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U20 Interaction | Interacting Bases [5,5] | 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 A21 Insertion | Location [2] | Length Distribution [0.005372012,0.322320709,0.016116035,0.644910019,0.010744024,0.000537201] | Letter Distribution [0.055555556,0.388888889,0.277777778,0.277777778,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2 Insertion | Location [4] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.100000000,0.300000000,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4Sequences of instances from HL_48810.1:
> HL_48810.1 HL_4RDX_001 C 13 G 22 CAGCUGGUUAG > HL_48810.1 HL_4RDX_004 C 13 G 22 CAGCUGGUUAG > HL_48810.1 HL_3WQY_001 C 1613 G 1622 CAGCGGGAG