Alignment of HL_56676.1 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
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distance
Interior
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Alignment
score
deficit
HL_56676.1_Instance_1 HL_56676.1,HL_8HNT_002,U103_G108UGUAAG
HL_56676.1_Sequence_1 HL_56676.18HNT_U103_G108UGUAAGtrue92000.74
HL_56676.1_Instance_2 HL_56676.1,HL_6DLR_001,C27_G32CUUCGG
HL_56676.1_Sequence_2 HL_56676.16DLR_C27_G32CUUCGGtrue100000.00

Conserved interactions between motif group positions in HL_56676.1:
1 2 s35 
1 6 cWW 
2 5 tSW 
2 6 s55 
3 4 s55 
5 6 s55
JAR3D SCFG/MRF model for HL_56676.1:
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 [[0.010391363,0.015542673,0.012620534,0.118031974,0.000000000],[0.161407275,0.018831736,0.135468706,0.014912387,0.000000000],[0.012838381,0.120099009,0.002697951,0.019069108,0.000000000],[0.143779637,0.013983083,0.188496931,0.011829251,0.000000000],[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 U103 - G108 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.024834525,0.023001162,0.003603828,0.169347657,0.000000000],[0.024449909,0.016539042,0.003603828,0.025477384,0.000000000],[0.127286807,0.003603828,0.003603828,0.017473363,0.000000000],[0.017874186,0.017341162,0.370186749,0.151772741,0.000000000],[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 [2] | Right Index [5] // Basepair G104 - A107 tSW 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U105:A106
Interaction  | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U105
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A106
Sequences of instances from HL_56676.1:
> HL_56676.1  8HNT U  103 G  108
UGUAAG
> HL_56676.1  6DLR C   27 G   32
CUUCGG