Alignment of HL_68529.1 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


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
HL_68529.1_Instance_1 HL_68529.1_HL_4OOG_002_G14_C19GAGUCC
HL_68529.1_Sequence_1 HL_68529.1_HL_4OOG_002_G14_C19GAGUCCtrue100000.00
HL_68529.1_Instance_2 HL_68529.1_HL_4OOG_001_G14_C19GAGUCC
HL_68529.1_Sequence_2 HL_68529.1_HL_4OOG_001_G14_C19GAGUCCtrue100000.00
HL_68529.1_Instance_3 HL_68529.1_HL_5T16_002_G16_C21GAGUCC
HL_68529.1_Sequence_3 HL_68529.1_HL_5T16_002_G16_C21GAGUCCtrue100000.00
HL_68529.1_Instance_4 HL_68529.1_HL_4KR9_001_G10_C15GUGUCC
HL_68529.1_Sequence_4 HL_68529.1_HL_4KR9_001_G10_C15GUGUCCtrue91000.85

Conserved interactions between motif group positions in HL_68529.1:
1 2 s35 
1 3 cWW 
2 3 s55 
JAR3D SCFG/MRF model for HL_68529.1:
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 [3] // Initial node G14 - C19 from junction 
BasepairNode | Deletion Probability [0.0000000000030849] | 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 [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.350000000,0.050000000,0.450000000,0.150000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Left Index [1] | Right Index [3] // Basepair G14 - C19 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node U17:U17
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U17
Sequences of instances from HL_68529.1:
> HL_68529.1 HL_4OOG_002 G   14 C   19
GAGUCC
> HL_68529.1 HL_4OOG_001 G   14 C   19
GAGUCC
> HL_68529.1 HL_5T16_002 G   16 C   21
GAGUCC
> HL_68529.1 HL_4KR9_001 G   10 C   15
GUGUCC