Alignment of HL_61984.1 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
2
I

6
2

3
7
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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distance

Alignment
score
deficit
HL_61984.1_Instance_1 HL_61984.1_HL_4O26_001_C186_G190CUCGG
HL_61984.1_Sequence_1 HL_61984.1_HL_4O26_001_C186_G190CUCGGtrue100000.00
HL_61984.1_Instance_2 HL_61984.1_HL_4V9F_021_C712_G716CUUUG
HL_61984.1_Sequence_2 HL_61984.1_HL_4V9F_021_C712_G716CUUUGtrue100000.00

Conserved interactions between motif group positions in HL_61984.1:
1 2 s35 
1 3 cWW 
2 3 s55 
JAR3D SCFG/MRF model for HL_61984.1:
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 [3] // Initial node C186 - G190 from junction 
BasepairNode | Deletion Probability [0.0000000006094467] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | 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 [1] | Right Index [3] // Basepair C186 - G190 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node C188:C188
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C188
Sequences of instances from HL_61984.1:
> HL_61984.1 HL_4O26_001 C  186 G  190
CUCGG
> HL_61984.1 HL_4V9F_021 C  712 G  716
CUUUG