Alignment of HL_27359.1 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
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Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_27359.1_Instance_1 HL_27359.1_HL_4TUE_033_C12_G22CAGCCUGGUAG
HL_27359.1_Sequence_1 HL_27359.1_HL_4TUE_033_C12_G22CAGCCUGGUAGtrue76003.90
HL_27359.1_Instance_2 HL_27359.1_HL_2ZZN_004_U13_A22UAGGGGCUA
HL_27359.1_Sequence_2 HL_27359.1_HL_2ZZN_004_U13_A22UAGGGGCUAtrue100000.00

Conserved interactions between motif group positions in HL_27359.1:
1 5 cWW 
2 3 s35 
2 4 cWS 
2 5 s55 
3 4 s55 
JAR3D SCFG/MRF model for HL_27359.1:
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 [5] // Initial node C12 - G22 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009285457,0.017323068,0.010436779,0.197555258,0.000000000],[0.021160175,0.009772202,0.212782490,0.012417770,0.000000000],[0.010508004,0.198766713,0.002067002,0.023256875,0.000000000],[0.212699647,0.011830790,0.040032900,0.010104868,0.000000000],[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 [5] // Basepair C12 - G22 cWW 
BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.209714169,0.183882729,0.194324745,0.286764507,0.000000000],[0.014692188,0.011983187,0.001999102,0.012161323,0.000000000],[0.019866299,0.001999102,0.025462132,0.009509275,0.000000000],[0.007136885,0.007528516,0.005957773,0.007018068,0.000000000],[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 [0.000000000,0.000000000,0.000000000,0.011890606,0.475624257,0.023781213,0.476218787,0.011890606,0.000594530] | Right Letter Distribution [0.041666667,0.291666667,0.458333333,0.208333333,0.000000000] | Left Index [2] | Right Index [4] // Basepair A13 - A21 cWS 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G14:G14
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],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[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 G14
Sequences of instances from HL_27359.1:
> HL_27359.1 HL_4TUE_033 C   12 G   22
CAGCCUGGUAG
> HL_27359.1 HL_2ZZN_004 U   13 A   22
UAGGGGCUA