Alignment of HL_80705.1 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
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
HL_80705.1_Instance_1 HL_80705.1_HL_3NKB_001_C20_G28CUCCUCGCG
HL_80705.1_Sequence_1 HL_80705.1_HL_3NKB_001_C20_G28CUCCUCGCGtrue100000.00
HL_80705.1_Instance_2 HL_80705.1_HL_4PR6_001_C119_G128CUCCUCGCUG
HL_80705.1_Sequence_2 HL_80705.1_HL_4PR6_001_C119_G128CUCCUCGCUGtrue93001.20

Conserved interactions between motif group positions in HL_80705.1:
1 2 s35 
1 7 cWW 
2 5 s35 
2 6 tWW 
2 7 s55 
3 4 s35 
5 6 s53 
6 7 s55 
5 4 7BPh
5 2 7BR
JAR3D SCFG/MRF model for HL_80705.1:
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 [7] // Initial node C20 - G28 from junction 
BasepairNode | Deletion Probability [0.0000000083615247] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [0.011890606,0.487514863,0.487514863,0.012485137,0.000594530] | Right Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C20 - G28 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.016132647,0.013222764,0.002925794,0.014423455,0.000000000],[0.268574183,0.013818458,0.012328290,0.013607089,0.000000000],[0.002925794,0.009504076,0.025714781,0.013537368,0.000000000],[0.234369790,0.014144852,0.312187293,0.032583365,0.000000000],[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 [6] // Basepair U21 - G26 tWW 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node C22:C25
Interaction  | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C22
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C23
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.906250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_80705.1:
> HL_80705.1 HL_3NKB_001 C   20 G   28
CUCCUCGCG
> HL_80705.1 HL_4PR6_001 C  119 G  128
CUCCUCGCUG