Alignment of HL_89082.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_89082.1
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
4
I

12
4

6
13
4
I

14
4

7
15
4
I

16
4

8
17
4
I

18
4

9
19
3
I

20
3

10
21
2
I

22
2

11
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_89082.1_Instance_1 HL_89082.1_HL_3EGZ_005_G12_C24GAAGAAUACGACC
HL_89082.1_Sequence_1 HL_89082.1_HL_3EGZ_005_G12_C24GAAGAAUACGACCtrue100000.00
HL_89082.1_Instance_2 HL_89082.1_HL_3EGZ_007_G12_C24GAAGAAUACGACC
HL_89082.1_Sequence_2 HL_89082.1_HL_3EGZ_007_G12_C24GAAGAAUACGACCtrue100000.00
HL_89082.1_Instance_3 HL_89082.1_HL_3EGZ_001_G12_C24GAAGAAUACGACC
HL_89082.1_Sequence_3 HL_89082.1_HL_3EGZ_001_G12_C24GAAGAAUACGACCtrue100000.00
HL_89082.1_Instance_4 HL_89082.1_HL_3EGZ_003_G12_C24GAAGAAUACGACC
HL_89082.1_Sequence_4 HL_89082.1_HL_3EGZ_003_G12_C24GAAGAAUACGACCtrue100000.00

Conserved interactions between motif group positions in HL_89082.1:
1 2 s35 
1 11 cWW 
2 3 s35 
2 10 cWW 
3 4 s35 
4 5 s35 
7 8 s35 
9 10 s35 
10 11 s35 
8 7 7BPh
4 8 6BPh
JAR3D SCFG/MRF model for HL_89082.1:
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 [11] // Initial node G12 - C24 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [11] // Basepair G12 - C24 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.013555679,0.330164293,0.011831118,0.031455458,0.000000000],[0.011882468,0.011387993,0.023871313,0.011757050,0.000000000],[0.011553315,0.028303234,0.002917028,0.266930641,0.000000000],[0.025035369,0.012901190,0.012338114,0.194115737,0.000000000],[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 [2] | Right Index [10] // Basepair A13 - C23 cWW 
HairpinNode  | Num Bases [7] | Left Index [3] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node A14:A22
Interaction  | Interacting Bases [1,1] | 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 A14
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.016666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.950000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[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 A16
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 U18
Interaction  | Interacting Bases [5,5] | 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 A19
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.950000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.016666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C20
Interaction  | Interacting Bases [7,7] | 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 A22
Insertion    | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3
Insertion    | Location [6] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 8, position 6
Sequences of instances from HL_89082.1:
> HL_89082.1 HL_3EGZ_005 G   12 C   24
GAAGAAUACGACC
> HL_89082.1 HL_3EGZ_007 G   12 C   24
GAAGAAUACGACC
> HL_89082.1 HL_3EGZ_001 G   12 C   24
GAAGAAUACGACC
> HL_89082.1 HL_3EGZ_003 G   12 C   24
GAAGAAUACGACC