Alignment of HL_17899.1 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
4
I

6
7

3
7
7
I

8
8

4
9
8
I

10
8

5
11
7
I

12
7

6
13
6
I

14
5

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_17899.1_Instance_1 HL_17899.1_HL_3IVN_002_G37_C44GUGUCUAC
HL_17899.1_Sequence_1 HL_17899.1_HL_3IVN_002_G37_C44GUGUCUACtrue100000.00

Conserved interactions between motif group positions in HL_17899.1:
1 2 s35 
1 8 cWW 
2 4 s35 
3 6 tSW 
3 7 s35 
5 6 s35 
6 7 s35 
7 8 s35 
2 1 7BPh
5 4 7BPh
5 3 7BR
JAR3D SCFG/MRF model for HL_17899.1:
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 [8] // Initial node G37 - C44 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G37 - C44 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.023113467,0.020138053,0.006415535,0.031225124,0.000000000],[0.020848871,0.026091785,0.006415535,0.069174162,0.000000000],[0.021038698,0.006415535,0.006415535,0.651454480,0.000000000],[0.020297547,0.028213891,0.031106081,0.031635702,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair G39 - U42 tSW 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U40:C41
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[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 U40
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.833333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C41
Sequences of instances from HL_17899.1:
> HL_17899.1 HL_3IVN_002 G   37 C   44
GUGUCUAC