Alignment of HL_58912.1 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
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
2
I

8
2

4
9
1
I


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Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_58912.1_Instance_1 HL_58912.1_HL_5NFV_001_C-10_G-5CUGUUG
HL_58912.1_Sequence_1 HL_58912.1_HL_5NFV_001_C-10_G-5CUGUUGtrue100000.00

Conserved interactions between motif group positions in HL_58912.1:
1 2 s35 
1 3 perp 
1 4 cWW 
2 3 perp 
2 4 s55 
4 3 2BR
JAR3D SCFG/MRF model for HL_58912.1:
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 [4] // Initial node C-10 - G-5 from junction 
BasepairNode | Deletion Probability [0.0000000005780646] | Pair Probability [[0.004779407,0.008570624,0.027472582,0.099626418,0.000000000],[0.010161837,0.004867687,0.533557704,0.006911397,0.000000000],[0.005556221,0.101773100,0.005236567,0.011760459,0.000000000],[0.100917975,0.006658998,0.067084168,0.005064856,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C-10 - G-5 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U-9:G-8
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[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-9
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G-8
Sequences of instances from HL_58912.1:
> HL_58912.1 HL_5NFV_001 C  -10 G   -5
CUGUUG