Alignment of HL_07480.2 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
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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Full
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Alignment
score
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HL_07480.2_Instance_1 HL_07480.2,HL_1U0B_001,A12_U23AAAGCGGUUAU
HL_07480.2_Sequence_1 HL_07480.21U0B_A12_U23AAAGCGGUUAUtrue100000.00
HL_07480.2_Instance_2 HL_07480.2,HL_9MTS_101,A12_U23AAAGCGGUUAU
HL_07480.2_Sequence_2 HL_07480.29MTS_A12_U23AAAGCGGUUAUtrue100000.00
HL_07480.2_Instance_3 HL_07480.2,HL_1B23_001,A12_U23AAAGCGGUUAU
HL_07480.2_Sequence_3 HL_07480.21B23_A12_U23AAAGCGGUUAUtrue100000.00

Conserved interactions between motif group positions in HL_07480.2:
1 2 s35 
1 7 cWW 
2 6 tSH 
3 4 s35 
3 6 s55 
4 5 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_07480.2:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009192800,0.021796849,0.009818110,0.231259682,0.000000000],[0.017348091,0.009487247,0.192280868,0.010258268,0.000000000],[0.009798999,0.194773596,0.002021335,0.052697140,0.000000000],[0.194120479,0.010921091,0.022789191,0.011436255,0.000000000],[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 [7] // Basepair A12 - U23 cWW 
BasepairNode | Deletion Probability [0.0000000000000150] | Pair Probability [[0.204320682,0.020445800,0.001751945,0.010683263,0.000000000],[0.169873944,0.069586054,0.001751945,0.001751945,0.000000000],[0.145942688,0.001751945,0.015218709,0.038237326,0.000000000],[0.157756201,0.157423665,0.001751945,0.001751945,0.000000000],[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 [0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.035714286,0.035714286,0.464285714,0.464285714,0.000000000] | Left Index [2] | Right Index [6] // Basepair A13 - A22 tSH 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [0.999999999999999] // Hairpin node A14:C16
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A14
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C16
Sequences of instances from HL_07480.2:
> HL_07480.2  1U0B A   12 U   23
AAAGCGGUUAU
> HL_07480.2  9MTS A   12 U   23
AAAGCGGUUAU
> HL_07480.2  1B23 A   12 U   23
AAAGCGGUUAU