Alignment of HL_62934.1 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
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Full
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Interior
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Alignment
score
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HL_62934.1_Instance_1 HL_62934.1,HL_8K0K_001,C42_G48CGCAUAG
HL_62934.1_Sequence_1 HL_62934.18K0K_C42_G48CGCAUAGtrue92000.72
HL_62934.1_Instance_2 HL_62934.1,HL_5J7L_140,C225_G230CAACCG
HL_62934.1_Sequence_2 HL_62934.15J7L_C225_G230CAACCGtrue100000.00

Conserved interactions between motif group positions in HL_62934.1:
1 2 s35 
1 6 cWW 
2 3 s35 
2 5 tSH 
5 6 s35 
5 2 6BR
JAR3D SCFG/MRF model for HL_62934.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | 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 [0.991950402,0.007999600,0.000049998] | 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 C42 - G48 cWW 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.068018222,0.169267883,0.001674576,0.007332813,0.000000000],[0.069319270,0.149176485,0.001674576,0.001674576,0.000000000],[0.165474515,0.001674576,0.007597281,0.084931583,0.000000000],[0.144999575,0.123834918,0.001674576,0.001674576,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair G43 - A47 tSH 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A45:U46
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 A45
Interaction  | Interacting Bases [2,2] | 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 U46
Sequences of instances from HL_62934.1:
> HL_62934.1  8K0K C   42 G   48
CGCAUAG
> HL_62934.1  5J7L C  225 G  230
CAACCG