Alignment of HL_02811.1 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
3
I

6
3

3
7
2
I

8
2

4
9
1
I


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Alignment
score
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HL_02811.1_Instance_1 HL_02811.1_HL_3TRZ_001_A5_U13AGGGAUUUU
HL_02811.1_Sequence_1 HL_02811.1_HL_3TRZ_001_A5_U13AGGGAUUUUtrue100000.00

Conserved interactions between motif group positions in HL_02811.1:
1 4 cWW 
JAR3D SCFG/MRF model for HL_02811.1:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [4] // Initial node A5 - U13 from junction 
BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.214285714,0.071428571,0.500000000,0.214285714,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair A5 - U13 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U11:U12
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U11
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U12
Sequences of instances from HL_02811.1:
> HL_02811.1 HL_3TRZ_001 A    5 U   13
AGGGAUUUU