Alignment of HL_82710.2 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
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_82710.2_Instance_1 HL_82710.2,HL_9DFE_003,G123_C128GGGAAC
HL_82710.2_Sequence_1 HL_82710.29DFE_G123_C128GGGAACtrue95000.51
HL_82710.2_Instance_2 HL_82710.2,HL_5J7L_136,G123_C128GGAAAC
HL_82710.2_Sequence_2 HL_82710.25J7L_G123_C128GGAAACtrue100000.00
HL_82710.2_Instance_3 HL_82710.2,HL_7A0S_003,G121_C126GGAAAC
HL_82710.2_Sequence_3 HL_82710.27A0S_G121_C126GGAAACtrue100000.00
HL_82710.2_Instance_4 HL_82710.2,HL_1U63_002,G20_C25GAACUC
HL_82710.2_Sequence_4 HL_82710.21U63_G20_C25GAACUCtrue73002.54

Conserved interactions between motif group positions in HL_82710.2:
1 2 s35 
1 5 cWW 
2 5 s55 
3 4 s35
JAR3D SCFG/MRF model for HL_82710.2:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000060823043662] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G123 - C128 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G124:A127
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.583333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G124
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A126
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A127
Insertion    | Location [1] | Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_82710.2:
> HL_82710.2  9DFE G  123 C  128
GGGAAC
> HL_82710.2  5J7L G  123 C  128
GGAAAC
> HL_82710.2  7A0S G  121 C  126
GGAAAC
> HL_82710.2  1U63 G   20 C   25
GAACUC