Alignment of HL_24792.1 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
3
I

4
4

2
5
4
I

6
4

3
7
3
I

8
2

4
9
2
I

10
2

5
11
2
I

12
2

6
13
1
I


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Alignment
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HL_24792.1_Instance_1 HL_24792.1,HL_6XJQ_003,G26_C35GCCCGUUAUC
HL_24792.1_Sequence_1 HL_24792.16XJQ_G26_C35GCCCGUUAUCtrue100000.00

Conserved interactions between motif group positions in HL_24792.1:
1 6 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
4 6 cWS 
5 6 s55 
4 1 7BPh
JAR3D SCFG/MRF model for HL_24792.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000381350679448848525461538405014458471171802] | Num Left Bases [1] | Num Right Bases [3] | Left Index [1] | Right Index [6] | Norm Constant [0.252874089601252] // Cluster node 6XJQ|1|A|G|26:6XJQ|1|A|G|26 and 6XJQ|1|A|C|29:6XJQ|1|A|C|35
Interaction  | Interacting Bases [1,4] | 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]] // Cluster Interaction 6XJQ|1|A|G|26 - 6XJQ|1|A|C|35 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.002803848,0.003708984,0.002495174,0.003379005,0.000000000],[0.308045541,0.337328559,0.003274276,0.315256992,0.000000000],[0.004112495,0.000467754,0.004931670,0.001873112,0.000000000],[0.002874091,0.004645558,0.002188090,0.002614851,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6XJQ|1|A|C|29 - 6XJQ|1|A|C|35 cWS 
Interaction  | Interacting Bases [3,3] | 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]] // Right strand conserved insertion 6XJQ|1|A|G|30
Insertion    | Location [3] | Length Distribution [0.000000000,0.000000000,0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000]// Insertion after nucleotide 5, position 3 in cluster node
InitialNode  | 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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C27:C28
Interaction  | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C27
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C28
Sequences of instances from HL_24792.1:
> HL_24792.1  6XJQ G   26 C   35
GCCCGUUAUC