Alignment of HL_50537.2 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
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_50537.2_Instance_1 HL_50537.2_HL_4WJ4_002_A31_U39ACUGUUAAU
HL_50537.2_Sequence_1 HL_50537.2_HL_4WJ4_002_A31_U39ACUGUUAAUtrue100000.00
HL_50537.2_Instance_2 HL_50537.2_HL_4WJ4_005_A31_U39ACUGUUAAU
HL_50537.2_Sequence_2 HL_50537.2_HL_4WJ4_005_A31_U39ACUGUUAAUtrue100000.00
HL_50537.2_Instance_3 HL_50537.2_HL_3KFU_005_G31_C39GCUGUUAAC
HL_50537.2_Sequence_3 HL_50537.2_HL_3KFU_005_G31_C39GCUGUUAACtrue100000.06

Conserved interactions between motif group positions in HL_50537.2:
1 2 s35 
1 8 cWW 
2 7 bif 
4 5 perp 
5 6 s35 
7 8 s35 
JAR3D SCFG/MRF model for HL_50537.2:
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 [8] // Initial node A31 - U39 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009341597,0.021222893,0.010204228,0.220628516,0.000000000],[0.017209227,0.009475562,0.195205747,0.011223855,0.000000000],[0.010150854,0.208524333,0.002037222,0.043966533,0.000000000],[0.195018545,0.011831944,0.022937162,0.011021781,0.000000000],[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 [8] // Basepair A31 - U39 cWW 
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.026873761,0.030189235,0.006557195,0.006557195,0.000000000],[0.731077818,0.076793656,0.006557195,0.006557195,0.000000000],[0.006557195,0.006557195,0.027515142,0.041978435,0.000000000],[0.006557195,0.006557195,0.006557195,0.006557195,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair C32 - A38 bif 
HairpinNode  | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U33:U36
Interaction  | Interacting Bases [1,1] | 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 U33
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[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 G34
Interaction  | Interacting Bases [3,3] | 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 U35
Interaction  | Interacting Bases [4,4] | 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 U36
Sequences of instances from HL_50537.2:
> HL_50537.2 HL_4WJ4_002 A   31 U   39
ACUGUUAAU
> HL_50537.2 HL_4WJ4_005 A   31 U   39
ACUGUUAAU
> HL_50537.2 HL_3KFU_005 G   31 C   39
GCUGUUAAC