Alignment of HL_37407.1 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
4

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
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Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_37407.1_Instance_1 HL_37407.1_HL_4V9F_019_G670_C676GAGUAUC
HL_37407.1_Sequence_1 HL_37407.1_HL_4V9F_019_G670_C676GAGUAUCtrue100000.00
HL_37407.1_Instance_2 HL_37407.1_HL_6CZR_076_G207_C213GCUUUGC
HL_37407.1_Sequence_2 HL_37407.1_HL_6CZR_076_G207_C213GCUUUGCtrue89001.33

Conserved interactions between motif group positions in HL_37407.1:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 tSH 
4 5 s35 
JAR3D SCFG/MRF model for HL_37407.1:
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 [5] // Initial node G670 - C676 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G670 - C676 cWW 
BasepairNode | Deletion Probability [0.0000000006094467] | Pair Probability [[0.023021455,0.015676229,0.003775280,0.387331964,0.000000000],[0.018776188,0.015711894,0.102705762,0.003775280,0.000000000],[0.017792908,0.003775280,0.340741106,0.022912277,0.000000000],[0.018571381,0.017882434,0.003775280,0.003775280,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair A671 - U675 tSH 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U673:U673
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 U673
Sequences of instances from HL_37407.1:
> HL_37407.1 HL_4V9F_019 G  670 C  676
GAGUAUC
> HL_37407.1 HL_6CZR_076 G  207 C  213
GCUUUGC