Alignment of HL_78677.1 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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Alignment
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HL_78677.1_Instance_1 HL_78677.1,HL_2CZJ_009,U26_G29UUCG
HL_78677.1_Sequence_1 HL_78677.12CZJ_U26_G29UUCGtrue100000.00
HL_78677.1_Instance_2 HL_78677.1,HL_8CRE_043,G2088_C2092GGUAC
HL_78677.1_Sequence_2 HL_78677.18CRE_G_2088_C_2092GGUACtrue89001.03

Conserved interactions between motif group positions in HL_78677.1:
1 3 cWW
JAR3D SCFG/MRF model for HL_78677.1:
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 [0.0000000078315923] | Pair Probability [[0.010489920,0.017127883,0.012680838,0.119297674,0.000000000],[0.159817824,0.018747803,0.122690376,0.014659067,0.000000000],[0.012775575,0.132830577,0.002697714,0.020718591,0.000000000],[0.142468525,0.014233330,0.186841746,0.011922559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair U26 - G29 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node U27:U27
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U27
Sequences of instances from HL_78677.1:
> HL_78677.1  2CZJ U   26 G   29
UUCG
> HL_78677.1  8CRE G 2088 C 2092
GGUAC