Alignment of HL_19162.2 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
4
I

12
4

6
13
4
I

14
4

7
15
4
I

16
4

8
17
4
I

18
4

9
19
4
I

20
4

10
21
3
I

22
3

11
23
2
I

24
2

12
25
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_19162.2_Instance_1 HL_19162.2_HL_3HHN_006_G1_C12GGAACACUAUAC
HL_19162.2_Sequence_1 HL_19162.2_HL_3HHN_006_G1_C12GGAACACUAUACtrue100000.00
HL_19162.2_Instance_2 HL_19162.2_HL_3IVK_001_G1_C12GGAACACUAUAC
HL_19162.2_Sequence_2 HL_19162.2_HL_3IVK_001_G1_C12GGAACACUAUACtrue100000.00
HL_19162.2_Instance_3 HL_19162.2_HL_2A64_006_C313_G324CGGCGCAUGCAG
HL_19162.2_Sequence_3 HL_19162.2_HL_2A64_006_C313_G324CGGCGCAUGCAGtrue80003.63

Conserved interactions between motif group positions in HL_19162.2:
1 2 s35 
1 12 cWW 
2 11 tSH 
2 12 s55 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
11 12 s35 
11 2 6BR
JAR3D SCFG/MRF model for HL_19162.2:
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 [12] // Initial node G1 - C12 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[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 [12] // Basepair G1 - C12 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.111651162,0.118197802,0.001340298,0.006316827,0.000000000],[0.112480650,0.117924104,0.001340298,0.001340298,0.000000000],[0.163155990,0.001340298,0.006552290,0.113759406,0.000000000],[0.124632514,0.117287469,0.001340298,0.001340298,0.000000000],[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 [2] | Right Index [11] // Basepair G2 - A11 tSH 
HairpinNode  | Num Bases [8] | Left Index [3] | Right Index [10] | Norm Constant [0.999999999999999] // Hairpin node A3:U10
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 A3
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[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 A4
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 C5
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[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 A6
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[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 C7
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U8
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 A9
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U10
Sequences of instances from HL_19162.2:
> HL_19162.2 HL_3HHN_006 G    1 C   12
GGAACACUAUAC
> HL_19162.2 HL_3IVK_001 G    1 C   12
GGAACACUAUAC
> HL_19162.2 HL_2A64_006 C  313 G  324
CGGCGCAUGCAG