Alignment of HL_18218.2 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
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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distance

Alignment
score
deficit
HL_18218.2_Instance_1 HL_18218.2_HL_2ZZM_002_G31_C39GCCUAGGAC
HL_18218.2_Sequence_1 HL_18218.2_HL_2ZZM_002_G31_C39GCCUAGGACtrue97000.27
HL_18218.2_Instance_2 HL_18218.2_HL_361D_002_G86_C90GGCGAC
HL_18218.2_Sequence_2 HL_18218.2_HL_361D_002_G86_C90GGCGACtrue100000.00

Conserved interactions between motif group positions in HL_18218.2:
1 2 s35 
1 6 cWW 
2 5 bif 
3 4 perp 
5 6 s35 
JAR3D SCFG/MRF model for HL_18218.2:
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 [6] // Initial node G31 - C39 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 G31 - C39 cWW 
BasepairNode | Deletion Probability [0.0000001006385525] | Pair Probability [[0.025903719,0.029099517,0.006320505,0.006320505,0.000000000],[0.641854421,0.074021693,0.006320505,0.006320505,0.000000000],[0.105250986,0.006320505,0.026521948,0.040463171,0.000000000],[0.006320505,0.006320505,0.006320505,0.006320505,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | 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 U34:G36
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 U34
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[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 G36
Insertion    | Location [1] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Sequences of instances from HL_18218.2:
> HL_18218.2 HL_2ZZM_002 G   31 C   39
GCCUAGGAC
> HL_18218.2 HL_361D_002 G   86 C   90
GGCGAC