Alignment of HL_30680.3 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
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Cutoff
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Full
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Interior
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Alignment
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HL_30680.3_Instance_1 HL_30680.3,HL_5FJC_001,G23_C29GACUGGC
HL_30680.3_Sequence_1 HL_30680.35FJC_G23_C29GACUGGCtrue100000.00
HL_30680.3_Instance_2 HL_30680.3,HL_4AOB_001,G23_C29GACUGGC
HL_30680.3_Sequence_2 HL_30680.34AOB_G23_C29GACUGGCtrue100000.00
HL_30680.3_Instance_3 HL_30680.3,HL_6MWN_004,G650_C656GCUGGAC
HL_30680.3_Sequence_3 HL_30680.36MWN_G650_C656GCUGGACtrue62003.57
HL_30680.3_Instance_4 HL_30680.3,HL_4KQY_001,G23_C29GACUGGC
HL_30680.3_Sequence_4 HL_30680.34KQY_G23_C29GACUGGCtrue100000.00
HL_30680.3_Instance_5 HL_30680.3,HL_3V7E_001,G23_C29GACUGGC
HL_30680.3_Sequence_5 HL_30680.33V7E_G23_C29GACUGGCtrue100000.00
HL_30680.3_Instance_6 HL_30680.3,HL_6VMY_003,G268_C274GUCCCGC
HL_30680.3_Sequence_6 HL_30680.36VMY_G268_C274GUCCCGCtrue84001.54
HL_30680.3_Instance_7 HL_30680.3,HL_5U30_002,U43_G49UUUCCAG
HL_30680.3_Sequence_7 HL_30680.35U30_U43_G49UUUCCAGtrue43005.44
HL_30680.3_Instance_8 HL_30680.3,HL_3HHN_009,G75_C82GUGGCAGC
HL_30680.3_Sequence_8 HL_30680.33HHN_G75_C82GUGGCAGCtrue73002.59
HL_30680.3_Instance_9 HL_30680.3,HL_4WF9_014,G456_C463GGACCAUC
HL_30680.3_Sequence_9 HL_30680.34WF9_G456_C463GGACCAUCtrue87001.21
HL_30680.3_Instance_10 HL_30680.3,HL_3IVK_004,G75_C82GUGGCAGC
HL_30680.3_Sequence_10 HL_30680.33IVK_G75_C82GUGGCAGCtrue73002.59
HL_30680.3_Instance_11 HL_30680.3,HL_9DFE_013,G410_C417GGACCACC
HL_30680.3_Sequence_11 HL_30680.39DFE_G410_C417GGACCACCtrue91000.88
HL_30680.3_Instance_12 HL_30680.3,HL_5J7L_146,G410_C417GGACCAUC
HL_30680.3_Sequence_12 HL_30680.35J7L_G410_C417GGACCAUCtrue87001.21
HL_30680.3_Instance_13 HL_30680.3,HL_7A0S_014,G423_C430GGACCACC
HL_30680.3_Sequence_13 HL_30680.37A0S_G423_C430GGACCACCtrue91000.88
HL_30680.3_Instance_14 HL_30680.3,HL_4OQU_002,G32_C40GACGGACAC
HL_30680.3_Sequence_14 HL_30680.34OQU_G32_C40GACGGACACtrue12008.37
HL_30680.3_Instance_15 HL_30680.3,HL_1WZ2_006,A934_U942ACUCAAGAU
HL_30680.3_Sequence_15 HL_30680.31WZ2_A934_U942ACUCAAGAUtrue16007.94

Conserved interactions between motif group positions in HL_30680.3:
1 7 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_30680.3:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [7] // Initial node
BasepairNode | Deletion Probability [0.0000007064610604] | Pair Probability [[0.008696140,0.017711213,0.009950764,0.177723521,0.000000000],[0.032067839,0.009556319,0.170051229,0.011771982,0.000000000],[0.009873482,0.287470734,0.001922209,0.024588388,0.000000000],[0.169461409,0.012118484,0.047640069,0.009396219,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.465764023,0.465985079,0.067941420,0.000298425,0.000011053] | Left Letter Distribution [0.136363636,0.136363636,0.409090909,0.318181818,0.000000000] | Right Length Distribution [0.930093541,0.069519013,0.000376377,0.000011070] | 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 [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.205882353,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.147058824,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.147058824,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A24
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.088235294,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.558823529,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.205882353,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.147058824,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.088235294,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.147058824,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.264705882,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U26
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.441176471,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.147058824,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.382352941,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G27
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.205882353,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.205882353,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.441176471,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.147058824,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G28
Sequences of instances from HL_30680.3:
> HL_30680.3  5FJC G   23 C   29
GACUGGC
> HL_30680.3  4AOB G   23 C   29
GACUGGC
> HL_30680.3  6MWN G  650 C  656
GCUGGAC
> HL_30680.3  4KQY G   23 C   29
GACUGGC
> HL_30680.3  3V7E G   23 C   29
GACUGGC
> HL_30680.3  6VMY G  268 C  274
GUCCCGC
> HL_30680.3  5U30 U   43 G   49
UUUCCAG
> HL_30680.3  3HHN G   75 C   82
GUGGCAGC
> HL_30680.3  4WF9 G  456 C  463
GGACCAUC
> HL_30680.3  3IVK G   75 C   82
GUGGCAGC
> HL_30680.3  9DFE G  410 C  417
GGACCACC
> HL_30680.3  5J7L G  410 C  417
GGACCAUC
> HL_30680.3  7A0S G  423 C  430
GGACCACC
> HL_30680.3  4OQU G   32 C   40
GACGGACAC
> HL_30680.3  1WZ2 A  934 U  942
ACUCAAGAU