Alignment of HL_80922.2 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
4

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
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Full
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Alignment
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HL_80922.2_Instance_1 HL_80922.2,HL_4V9F_019,G670_C676GAGUAUC
HL_80922.2_Sequence_1 HL_80922.24V9F_G670_C676GAGUAUCtrue100000.00
HL_80922.2_Instance_2 HL_80922.2,HL_2B3J_001,A31_U39ACUACGGAU
HL_80922.2_Sequence_2 HL_80922.22B3J_A31_U39ACUACGGAUtrue60003.83
HL_80922.2_Instance_3 HL_80922.2,HL_5J7L_151,C611_G617CGAAUAG
HL_80922.2_Sequence_3 HL_80922.25J7L_C611_G617CGAAUAGtrue96000.42

Conserved interactions between motif group positions in HL_80922.2:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 tSH 
4 5 s35
JAR3D SCFG/MRF model for HL_80922.2:
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 [0.0000234451146992] | Pair Probability [[0.009425327,0.019602391,0.010550535,0.209161741,0.000000000],[0.018119710,0.009519290,0.209803050,0.012356683,0.000000000],[0.010544174,0.210633518,0.002053265,0.034146945,0.000000000],[0.196782200,0.012577586,0.024177876,0.010545706,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.0000000000179657] | Pair Probability [[0.065109001,0.064416304,0.002596566,0.208549605,0.000000000],[0.119242696,0.064304472,0.002596566,0.002596566,0.000000000],[0.082762049,0.002596566,0.179870726,0.066056294,0.000000000],[0.068982237,0.065127223,0.002596566,0.002596566,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.010744024,0.644641418,0.016116035,0.322857910,0.005372012,0.000268601] | Left Letter Distribution [0.357142857,0.214285714,0.214285714,0.214285714,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | 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 [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U673
Sequences of instances from HL_80922.2:
> HL_80922.2  4V9F G  670 C  676
GAGUAUC
> HL_80922.2  2B3J A   31 U   39
ACUACGGAU
> HL_80922.2  5J7L C  611 G  617
CGAAUAG