Alignment of HL_18722.1 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
3

3
7
2
I

8
2

4
9
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_18722.1_Instance_1 HL_18722.1_HL_4LFB_018_G838_C848GUCUC
HL_18722.1_Sequence_1 HL_18722.1_HL_4LFB_018_G838_C848GUCUCtrue100000.00
HL_18722.1_Instance_2 HL_18722.1_HL_6CZR_089_G822_C826GUCUC
HL_18722.1_Sequence_2 HL_18722.1_HL_6CZR_089_G822_C826GUCUCtrue100000.00
HL_18722.1_Instance_3 HL_18722.1_HL_6U8D_003_C232_G235CGUG
HL_18722.1_Sequence_3 HL_18722.1_HL_6U8D_003_C232_G235CGUGtrue87001.27

Conserved interactions between motif group positions in HL_18722.1:
1 3 s35 
1 4 cWW 
JAR3D SCFG/MRF model for HL_18722.1:
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 [4] // Initial node G838 - C848 from junction 
BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair G838 - C848 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U839:C840
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U839
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C840
Sequences of instances from HL_18722.1:
> HL_18722.1 HL_4LFB_018 G  838 C  848
GUCUC
> HL_18722.1 HL_6CZR_089 G  822 C  826
GUCUC
> HL_18722.1 HL_6U8D_003 C  232 G  235
CGUG