Alignment of HL_94386.1 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
3
I

8
3

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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Alignment
score
deficit
HL_94386.1_Instance_1 HL_94386.1_HL_6N5P_002_G58_C64GUGAAGC
HL_94386.1_Sequence_1 HL_94386.1_HL_6N5P_002_G58_C64GUGAAGCtrue76002.27
HL_94386.1_Instance_2 HL_94386.1_HL_2A64_001_G31_C36GGUUUC
HL_94386.1_Sequence_2 HL_94386.1_HL_2A64_001_G31_C36GGUUUCtrue100000.00
HL_94386.1_Instance_3 HL_94386.1_HL_361D_001_G86_C90GGCGAC
HL_94386.1_Sequence_3 HL_94386.1_HL_361D_001_G86_C90GGCGACtrue95000.51
HL_94386.1_Instance_4 HL_94386.1_HL_5TBW_012_C543_G548CCUCGG
HL_94386.1_Sequence_4 HL_94386.1_HL_5TBW_012_C543_G548CCUCGGtrue99000.10

Conserved interactions between motif group positions in HL_94386.1:
1 2 s35 
1 6 cWW 
5 6 s35 
JAR3D SCFG/MRF model for HL_94386.1:
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 [6] // Initial node G58 - C64 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009498175,0.019104591,0.010841350,0.196828520,0.000000000],[0.017548139,0.009402467,0.210196267,0.013152764,0.000000000],[0.010780994,0.232320656,0.002049218,0.025441577,0.000000000],[0.195565178,0.013399649,0.023821386,0.010049069,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair G58 - C64 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U59:G63
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U59
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A61
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A62
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G63
Insertion    | Location [1] | Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_94386.1:
> HL_94386.1 HL_6N5P_002 G   58 C   64
GUGAAGC
> HL_94386.1 HL_2A64_001 G   31 C   36
GGUUUC
> HL_94386.1 HL_361D_001 G   86 C   90
GGCGAC
> HL_94386.1 HL_5TBW_012 C  543 G  548
CCUCGG