Alignment of HL_60140.1 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
4
I

8
4

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_60140.1_Instance_1 HL_60140.1_HL_5WT1_002_A31_U39ACUGAAGAU
HL_60140.1_Sequence_1 HL_60140.1_HL_5WT1_002_A31_U39ACUGAAGAUtrue100000.00
HL_60140.1_Instance_2 HL_60140.1_HL_7A0S_041_G1646_C1653GUCAAUGC
HL_60140.1_Sequence_2 HL_60140.1_HL_7A0S_041_G_1646_C_1653GUCAAUGCtrue95000.60

Conserved interactions between motif group positions in HL_60140.1:
1 2 s35 
1 6 cWW 
2 5 bif 
3 4 s35 
4 5 s35 
5 6 s35 
JAR3D SCFG/MRF model for HL_60140.1:
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 [6] // Initial node A31 - U39 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009508309,0.021141169,0.010499222,0.212521883,0.000000000],[0.017307832,0.009562561,0.198596306,0.011821420,0.000000000],[0.010428025,0.212609503,0.002065216,0.039989476,0.000000000],[0.197383927,0.012407836,0.023236747,0.010920569,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair A31 - U39 cWW 
BasepairNode | Deletion Probability [0.0000000000430944] | Pair Probability [[0.025903719,0.029099517,0.006320505,0.006320505,0.000000000],[0.641854421,0.074021693,0.006320505,0.006320505,0.000000000],[0.006320505,0.006320505,0.026521948,0.040463171,0.000000000],[0.006320505,0.006320505,0.105250986,0.006320505,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.011890606,0.487514863,0.487514863,0.012485137,0.000594530] | Left Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair C32 - A38 bif 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A35:A36
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A36
Sequences of instances from HL_60140.1:
> HL_60140.1 HL_5WT1_002 A   31 U   39
ACUGAAGAU
> HL_60140.1 HL_7A0S_041 G 1646 C 1653
GUCAAUGC