Alignment of HL_89199.2 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
3

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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Alignment
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HL_89199.2_Instance_1 HL_89199.2,HL_2QUW_002,C32_G37CUGAUG
HL_89199.2_Sequence_1 HL_89199.22QUW_C32_G37CUGAUGtrue100000.00
HL_89199.2_Instance_2 HL_89199.2,HL_2QUS_002,C32_G37CUGAUG
HL_89199.2_Sequence_2 HL_89199.22QUS_C32_G37CUGAUGtrue100000.00
HL_89199.2_Instance_3 HL_89199.2,HL_5DH6_001,C16_G21CUGAUG
HL_89199.2_Sequence_3 HL_89199.25DH6_C16_G21CUGAUGtrue100000.00
HL_89199.2_Instance_4 HL_89199.2,HL_2OEU_001,C15_G20CUGAUG
HL_89199.2_Sequence_4 HL_89199.22OEU_C15_G20CUGAUGtrue100000.00
HL_89199.2_Instance_5 HL_89199.2,HL_8SYK_001,C22_G27CUGAUG
HL_89199.2_Sequence_5 HL_89199.28SYK_C22_G27CUGAUGtrue100000.00

Conserved interactions between motif group positions in HL_89199.2:
1 4 s35 
1 5 cWW 
2 3 s35 
3 5 perp 
4 5 s55
JAR3D SCFG/MRF model for HL_89199.2:
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 [0.0000001230289089] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair C32 - G37 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G34:U36
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.785714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G34
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U36
Sequences of instances from HL_89199.2:
> HL_89199.2  2QUW C   32 G   37
CUGAUG
> HL_89199.2  2QUS C   32 G   37
CUGAUG
> HL_89199.2  5DH6 C   16 G   21
CUGAUG
> HL_89199.2  2OEU C   15 G   20
CUGAUG
> HL_89199.2  8SYK C   22 G   27
CUGAUG