Alignment of HL_05692.1 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
2
I

6
2

3
7
1
I


In
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Interior
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Alignment
score
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HL_05692.1_Instance_1 HL_05692.1_HL_1WZ2_007_C950_G955CGUAGG
HL_05692.1_Sequence_1 HL_05692.1_HL_1WZ2_007_C950_G955CGUAGGtrue100000.00

Conserved interactions between motif group positions in HL_05692.1:
1 2 s35 
1 3 cWW 
2 3 s55 
JAR3D SCFG/MRF model for HL_05692.1:
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 [3] // Initial node C950 - G955 from junction 
BasepairNode | Deletion Probability [0.0000000000028903] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [0.000000000,0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair C950 - G955 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node G951:G951
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],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[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 G951
Sequences of instances from HL_05692.1:
> HL_05692.1 HL_1WZ2_007 C  950 G  955
CGUAGG