Alignment of HL_06569.1 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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Full
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Interior
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Alignment
score
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HL_06569.1_Instance_1 HL_06569.1_HL_7A0S_007_A202_U207AGAAUU
HL_06569.1_Sequence_1 HL_06569.1_HL_7A0S_007_A202_U207AGAAUUtrue100000.00
HL_06569.1_Instance_2 HL_06569.1_HL_4Y4O_109_A225_U230AGAAAU
HL_06569.1_Sequence_2 HL_06569.1_HL_4Y4O_109_A225_U230AGAAAUtrue95000.51
HL_06569.1_Instance_3 HL_06569.1_HL_4C9D_002_C21_G25CGUAG
HL_06569.1_Sequence_3 HL_06569.1_HL_4C9D_002_C21_G25CGUAGtrue91000.88
HL_06569.1_Instance_4 HL_06569.1_HL_5TBW_075_C108_G114CACAUUG
HL_06569.1_Sequence_4 HL_06569.1_HL_5TBW_075_C108_G114CACAUUGtrue63003.48

Conserved interactions between motif group positions in HL_06569.1:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 tSH 
3 4 s55 
4 5 s35 
JAR3D SCFG/MRF model for HL_06569.1:
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 A202 - U207 from junction 
BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.009228795,0.019179884,0.010238170,0.216808949,0.000000000],[0.018533875,0.009460985,0.216925123,0.011842533,0.000000000],[0.010289084,0.196034129,0.002025733,0.037602685,0.000000000],[0.194873981,0.011923789,0.024413241,0.010619045,0.000000000],[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 [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair A202 - U207 cWW 
BasepairNode | Deletion Probability [0.0000060823043662] | Pair Probability [[0.107010574,0.113285114,0.001284591,0.046687034,0.000000000],[0.107805585,0.113022792,0.001284591,0.001284591,0.000000000],[0.157305214,0.001284591,0.006279955,0.109031193,0.000000000],[0.119452378,0.112412618,0.001284591,0.001284591,0.000000000],[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 [0.741082411,0.255227552,0.003536285,0.000153752] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [4] // Basepair G203 - A205 tSH 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A204:A204
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A204
Sequences of instances from HL_06569.1:
> HL_06569.1 HL_7A0S_007 A  202 U  207
AGAAUU
> HL_06569.1 HL_4Y4O_109 A  225 U  230
AGAAAU
> HL_06569.1 HL_4C9D_002 C   21 G   25
CGUAG
> HL_06569.1 HL_5TBW_075 C  108 G  114
CACAUUG