Alignment of HL_81100.2 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
2

2
5
1
I


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Alignment
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HL_81100.2_Instance_1 HL_81100.2,HL_2Y8Y_001,C11_G16CGCGUG
HL_81100.2_Sequence_1 HL_81100.22Y8Y_C11_G16CGCGUGtrue100000.00
HL_81100.2_Instance_2 HL_81100.2,HL_2Y8W_001,C11_G16CGCGUG
HL_81100.2_Sequence_2 HL_81100.22Y8W_C11_G16CGCGUGtrue100000.00
HL_81100.2_Instance_3 HL_81100.2,HL_4WF9_009,G283_C288GCUUGC
HL_81100.2_Sequence_3 HL_81100.24WF9_G283_C288GCUUGCtrue97000.25

Conserved interactions between motif group positions in HL_81100.2:
1 2 cWW
JAR3D SCFG/MRF model for HL_81100.2:
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 [2] // Initial node
HairpinNode  | Num Bases [2] | Left Index [1] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node C11:G16
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C11 - G16 cWW 
Insertion    | Location [1] | Length Distribution [0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.035714286,0.250000000,0.392857143,0.321428571,0.000000000]// Insertion in Hairpin after nucleotide 1, position 1
Sequences of instances from HL_81100.2:
> HL_81100.2  2Y8Y C   11 G   16
CGCGUG
> HL_81100.2  2Y8W C   11 G   16
CGCGUG
> HL_81100.2  4WF9 G  283 C  288
GCUUGC