Alignment of HL_32512.6 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
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_32512.6_Instance_1 HL_32512.6_HL_4AOB_001_G23_C29GACUGGC
HL_32512.6_Sequence_1 HL_32512.6_HL_4AOB_001_G23_C29GACUGGCtrue100000.00
HL_32512.6_Instance_2 HL_32512.6_HL_4AOB_004_G23_C29GACUGGC
HL_32512.6_Sequence_2 HL_32512.6_HL_4AOB_004_G23_C29GACUGGCtrue100000.00
HL_32512.6_Instance_3 HL_32512.6_HL_5FJC_001_G23_C29GACUGGC
HL_32512.6_Sequence_3 HL_32512.6_HL_5FJC_001_G23_C29GACUGGCtrue100000.00
HL_32512.6_Instance_4 HL_32512.6_HL_4KQY_004_G23_C29GACUGGC
HL_32512.6_Sequence_4 HL_32512.6_HL_4KQY_004_G23_C29GACUGGCtrue100000.00
HL_32512.6_Instance_5 HL_32512.6_HL_4KQY_001_G23_C29GACUGGC
HL_32512.6_Sequence_5 HL_32512.6_HL_4KQY_001_G23_C29GACUGGCtrue100000.00
HL_32512.6_Instance_6 HL_32512.6_HL_3V7E_001_G23_C29GACUGGC
HL_32512.6_Sequence_6 HL_32512.6_HL_3V7E_001_G23_C29GACUGGCtrue100000.00
HL_32512.6_Instance_7 HL_32512.6_HL_6MWN_004_G650_C656GCUGGAC
HL_32512.6_Sequence_7 HL_32512.6_HL_6MWN_004_G650_C656GCUGGACtrue51005.25
HL_32512.6_Instance_8 HL_32512.6_HL_3HHN_009_G75_C82GUGGCAGC
HL_32512.6_Sequence_8 HL_32512.6_HL_3HHN_009_G75_C82GUGGCAGCtrue63003.89
HL_32512.6_Instance_9 HL_32512.6_HL_3IVK_004_G75_C82GUGGCAGC
HL_32512.6_Sequence_9 HL_32512.6_HL_3IVK_004_G75_C82GUGGCAGCtrue63003.89
HL_32512.6_Instance_10 HL_32512.6_HL_5U30_002_U43_G49UUUCCAG
HL_32512.6_Sequence_10 HL_32512.6_HL_5U30_002_U43_G49UUUCCAGtrue34007.01
HL_32512.6_Instance_11 HL_32512.6_HL_6VMY_003_G268_C274GUCCCGC
HL_32512.6_Sequence_11 HL_32512.6_HL_6VMY_003_G268_C274GUCCCGCtrue79002.27
HL_32512.6_Instance_12 HL_32512.6_HL_4WF9_014_G456_C463GGACCAUC
HL_32512.6_Sequence_12 HL_32512.6_HL_4WF9_014_G456_C463GGACCAUCtrue81002.01
HL_32512.6_Instance_13 HL_32512.6_HL_4Y4O_116_G410_C417GGACCACC
HL_32512.6_Sequence_13 HL_32512.6_HL_4Y4O_116_G410_C417GGACCACCtrue84001.67
HL_32512.6_Instance_14 HL_32512.6_HL_5J7L_146_G410_C417GGACCAUC
HL_32512.6_Sequence_14 HL_32512.6_HL_5J7L_146_G410_C417GGACCAUCtrue81002.01
HL_32512.6_Instance_15 HL_32512.6_HL_4OQU_002_G32_C40GACGGACAC
HL_32512.6_Sequence_15 HL_32512.6_HL_4OQU_002_G32_C40GACGGACACtrue6009.98
HL_32512.6_Instance_16 HL_32512.6_HL_7A0S_014_G423_C430GGACCACC
HL_32512.6_Sequence_16 HL_32512.6_HL_7A0S_014_G423_C430GGACCACCtrue84001.67

Conserved interactions between motif group positions in HL_32512.6:
1 7 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
JAR3D SCFG/MRF model for HL_32512.6:
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 G23 - C29 from junction 
BasepairNode | Deletion Probability [0.0000017102807318] | Pair Probability [[0.008642056,0.017479640,0.009921850,0.168007953,0.000000000],[0.030720937,0.009404426,0.169693359,0.011831898,0.000000000],[0.009837554,0.303581170,0.001904001,0.022870291,0.000000000],[0.168572384,0.012172502,0.046130308,0.009229670,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.561258214,0.437225398,0.001448346,0.000068043] | Left Letter Distribution [0.166666667,0.055555556,0.500000000,0.277777778,0.000000000] | Right Length Distribution [0.934446650,0.065203005,0.000340613,0.000009732] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [7] // Basepair G23 - C29 cWW 
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A24:G28
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.138888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.138888889,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.138888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A24
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.027777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.638888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.194444444,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.138888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.027777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.472222222,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.138888889,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.361111111,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U26
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.138888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.027777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G27
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.138888889,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.194444444,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.527777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.138888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G28
Sequences of instances from HL_32512.6:
> HL_32512.6 HL_4AOB_001 G   23 C   29
GACUGGC
> HL_32512.6 HL_4AOB_004 G   23 C   29
GACUGGC
> HL_32512.6 HL_5FJC_001 G   23 C   29
GACUGGC
> HL_32512.6 HL_4KQY_004 G   23 C   29
GACUGGC
> HL_32512.6 HL_4KQY_001 G   23 C   29
GACUGGC
> HL_32512.6 HL_3V7E_001 G   23 C   29
GACUGGC
> HL_32512.6 HL_6MWN_004 G  650 C  656
GCUGGAC
> HL_32512.6 HL_3HHN_009 G   75 C   82
GUGGCAGC
> HL_32512.6 HL_3IVK_004 G   75 C   82
GUGGCAGC
> HL_32512.6 HL_5U30_002 U   43 G   49
UUUCCAG
> HL_32512.6 HL_6VMY_003 G  268 C  274
GUCCCGC
> HL_32512.6 HL_4WF9_014 G  456 C  463
GGACCAUC
> HL_32512.6 HL_4Y4O_116 G  410 C  417
GGACCACC
> HL_32512.6 HL_5J7L_146 G  410 C  417
GGACCAUC
> HL_32512.6 HL_4OQU_002 G   32 C   40
GACGGACAC
> HL_32512.6 HL_7A0S_014 G  423 C  430
GGACCACC