Alignment of HL_55046.1 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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Alignment
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HL_55046.1_Instance_1 HL_55046.1_HL_2OZB_001_G35_C41GUUUAUC
HL_55046.1_Sequence_1 HL_55046.1_HL_2OZB_001_G35_C41GUUUAUCtrue100000.00

Conserved interactions between motif group positions in HL_55046.1:
1 4 s35 
1 5 cWW 
2 3 s35 
4 5 s55 
4 2 6BPh
4 3 7BPh
JAR3D SCFG/MRF model for HL_55046.1:
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 G35 - C41 from junction 
BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[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 [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G35 - C41 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U36:A39
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 U36
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],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[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 U37
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.970588235,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009803922,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009803922,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A39
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_55046.1:
> HL_55046.1 HL_2OZB_001 G   35 C   41
GUUUAUC