Alignment of HL_38168.1 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


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HL_38168.1_Instance_1 HL_38168.1,HL_8J72_001,C4_G8CAAAG
HL_38168.1_Sequence_1 HL_38168.18J72_C4_G8CAAAGtrue100000.00
HL_38168.1_Instance_2 HL_38168.1,HL_9H1K_001,C2551_G2557CUGUUCG
HL_38168.1_Sequence_2 HL_38168.19H1K_C_2551_G_2557CUGUUCGtrue69002.98

Conserved interactions between motif group positions in HL_38168.1:
1 3 cWW 
2 3 s55
JAR3D SCFG/MRF model for HL_38168.1:
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 [3] // Initial node
BasepairNode | Deletion Probability [0.0000000000026820] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Right Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair C4 - G8 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A7:A7
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A7
Sequences of instances from HL_38168.1:
> HL_38168.1  8J72 C    4 G    8
CAAAG
> HL_38168.1  9H1K C 2551 G 2557
CUGUUCG