Alignment of HL_62869.2 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
3

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
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region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
HL_62869.2_Instance_1 HL_62869.2_HL_4Y4O_105_G123_C128GGGAAC
HL_62869.2_Sequence_1 HL_62869.2_HL_4Y4O_105_G123_C128GGGAACtrue91000.85
HL_62869.2_Instance_2 HL_62869.2_HL_5J7L_136_G123_C128GGAAAC
HL_62869.2_Sequence_2 HL_62869.2_HL_5J7L_136_G123_C128GGAAACtrue100000.00
HL_62869.2_Instance_3 HL_62869.2_HL_7A0S_003_G121_C126GGAAAC
HL_62869.2_Sequence_3 HL_62869.2_HL_7A0S_003_G121_C126GGAAACtrue100000.00
HL_62869.2_Instance_4 HL_62869.2_HL_4WF9_003_G122_C127GGAAAC
HL_62869.2_Sequence_4 HL_62869.2_HL_4WF9_003_G122_C127GGAAACtrue100000.00

Conserved interactions between motif group positions in HL_62869.2:
1 2 s35 
1 5 cWW 
2 5 s55 
3 4 s35 
2 3 6BR
JAR3D SCFG/MRF model for HL_62869.2:
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 [5] // Initial node G123 - C128 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G123 - C128 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G124:A127
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.022727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.022727273,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.931818182,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.022727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G124
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A126
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A127
Insertion    | Location [1] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_62869.2:
> HL_62869.2 HL_4Y4O_105 G  123 C  128
GGGAAC
> HL_62869.2 HL_5J7L_136 G  123 C  128
GGAAAC
> HL_62869.2 HL_7A0S_003 G  121 C  126
GGAAAC
> HL_62869.2 HL_4WF9_003 G  122 C  127
GGAAAC