Alignment of HL_17086.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_17086.2
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
5
I

8
8

4
9
8
I

10
11

5
11
11
I

12
12

6
13
12
I

14
12

7
15
11
I

16
11

8
17
10
I

18
9

9
19
8
I

20
8

10
21
7
I

22
6

11
23
3
I

24
3

12
25
2
I

26
2

13
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_17086.2_Instance_1 HL_17086.2_HL_4V88_199_A520_U532AAUGUAAAUACCU
HL_17086.2_Sequence_1 HL_17086.2_HL_4V88_199_A520_U532AAUGUAAAUACCUtrue95001.03
HL_17086.2_Instance_2 HL_17086.2_HL_4WFL_001_G19_C31GAGGUAGCGGUGC
HL_17086.2_Sequence_2 HL_17086.2_HL_4WFL_001_G19_C31GAGGUAGCGGUGCtrue100000.00
HL_17086.2_Instance_3 HL_17086.2_HL_6GSL_221_C30_G42CGGCUACGAACCG
HL_17086.2_Sequence_3 HL_17086.2_HL_6GSL_221_C30_G42CGGCUACGAACCGtrue89002.11

Conserved interactions between motif group positions in HL_17086.2:
1 2 s35 
1 13 cWW 
2 3 s35 
2 12 cWW 
3 4 s35 
3 12 s55 
4 5 s35 
4 10 tSH 
5 8 tSH 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
11 12 s35 
12 13 s35 
5 8 6BPh
JAR3D SCFG/MRF model for HL_17086.2:
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 [13] // Initial node A520 - U532 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009425327,0.019602391,0.010550535,0.209161741,0.000000000],[0.018119710,0.009519290,0.209803050,0.012356683,0.000000000],[0.010544174,0.210633518,0.002053265,0.034146945,0.000000000],[0.196782200,0.012577586,0.024177876,0.010545706,0.000000000],[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 [13] // Basepair A520 - U532 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.017607393,0.119394744,0.136092483,0.082809975,0.000000000],[0.014346098,0.010186641,0.081282465,0.022340555,0.000000000],[0.121590058,0.094500843,0.002858877,0.103916014,0.000000000],[0.079787439,0.023683905,0.017024915,0.072577594,0.000000000],[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 [12] // Basepair A521 - C531 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [1] | Left Index [3] | Right Index [11] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [4] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.069626847,0.064428939,0.002533033,0.174024460,0.000000000],[0.122650945,0.064475214,0.002533033,0.002533033,0.000000000],[0.082795499,0.002533033,0.202308523,0.067747645,0.000000000],[0.071059593,0.065684135,0.002533033,0.002533033,0.000000000],[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 [4] | Right Index [10] // Basepair G523 - A529 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Position [2] | Left Index [5] | Right Index [9] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [5] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.044562893,0.036337907,0.000495420,0.002391071,0.000000000],[0.045035112,0.042298318,0.000495420,0.000495420,0.000000000],[0.044687019,0.000495420,0.002812122,0.030262453,0.000000000],[0.343146052,0.343608673,0.059408762,0.003467939,0.000000000],[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 [5] | Right Index [8] // Basepair U524 - A527 tSH 
HairpinNode  | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A525:A526
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A525
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[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 A526
Sequences of instances from HL_17086.2:
> HL_17086.2 HL_4V88_199 A  520 U  532
AAUGUAAAUACCU
> HL_17086.2 HL_4WFL_001 G   19 C   31
GAGGUAGCGGUGC
> HL_17086.2 HL_6GSL_221 C   30 G   42
CGGCUACGAACCG