Alignment of HL_29487.1 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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_29487.1_Instance_1 HL_29487.1_HL_2QUS_002_C32_G37CUGAUG
HL_29487.1_Sequence_1 HL_29487.1_HL_2QUS_002_C32_G37CUGAUGtrue100000.00
HL_29487.1_Instance_2 HL_29487.1_HL_2QUW_002_C32_G37CUGAUG
HL_29487.1_Sequence_2 HL_29487.1_HL_2QUW_002_C32_G37CUGAUGtrue100000.00
HL_29487.1_Instance_3 HL_29487.1_HL_5DH6_001_C16_G21CUGAUG
HL_29487.1_Sequence_3 HL_29487.1_HL_5DH6_001_C16_G21CUGAUGtrue100000.00
HL_29487.1_Instance_4 HL_29487.1_HL_2OEU_001_C15_G20CUGAUG
HL_29487.1_Sequence_4 HL_29487.1_HL_2OEU_001_C15_G20CUGAUGtrue100000.00

Conserved interactions between motif group positions in HL_29487.1:
1 2 perp 
1 5 s35 
1 6 cWW 
3 4 s35 
4 6 perp 
5 6 s55 
2 5 6BPh
JAR3D SCFG/MRF model for HL_29487.1:
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 [6] // Initial node C32 - G37 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C32 - G37 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U33:U36
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.016666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.016666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.950000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Interaction  | Interacting Bases [4,4] | 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 U36
Sequences of instances from HL_29487.1:
> HL_29487.1 HL_2QUS_002 C   32 G   37
CUGAUG
> HL_29487.1 HL_2QUW_002 C   32 G   37
CUGAUG
> HL_29487.1 HL_5DH6_001 C   16 G   21
CUGAUG
> HL_29487.1 HL_2OEU_001 C   15 G   20
CUGAUG