Alignment of HL_42998.2 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
3
I

14
3

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_42998.2_Instance_1 HL_42998.2,HL_5J7L_160,G978_C985GAAACAAC
HL_42998.2_Sequence_1 HL_42998.25J7L_G978_C985GAAACAACtrue98000.25
HL_42998.2_Instance_2 HL_42998.2,HL_4WF9_028,G1022_C1029GAAACAGC
HL_42998.2_Sequence_2 HL_42998.24WF9_G_1022_C_1029GAAACAGCtrue86001.72
HL_42998.2_Instance_3 HL_42998.2,HL_7A0S_027,G989_C996GAAACAAC
HL_42998.2_Sequence_3 HL_42998.27A0S_G989_C996GAAACAACtrue98000.25
HL_42998.2_Instance_4 HL_42998.2,HL_9DFE_026,G978_C985GGAACAAC
HL_42998.2_Sequence_4 HL_42998.29DFE_G978_C985GGAACAACtrue100000.00
HL_42998.2_Instance_5 HL_42998.2,HL_4V9F_029,G1076_C1083GGAACAAC
HL_42998.2_Sequence_5 HL_42998.24V9F_G_1076_C_1083GGAACAACtrue100000.00
HL_42998.2_Instance_6 HL_42998.2,HL_8CRE_025,G1144_C1151GGAUGAAC
HL_42998.2_Sequence_6 HL_42998.28CRE_G_1144_C_1151GGAUGAACtrue86001.68
HL_42998.2_Instance_7 HL_42998.2,HL_8P9A_138,G1148_C1155GGAUGAAC
HL_42998.2_Sequence_7 HL_42998.28P9A_G_1148_C_1155GGAUGAACtrue86001.68

Conserved interactions between motif group positions in HL_42998.2:
1 2 s35 
1 8 cWW 
2 5 s33 
2 8 s55 
3 4 s35 
4 5 perp 
6 7 s35 
5 4 7BPh
8 7 7BPh
JAR3D SCFG/MRF model for HL_42998.2:
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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003645200,0.053141532,0.004150910,0.075393230,0.000000000],[0.006402894,0.025021395,0.076032072,0.004974767,0.000000000],[0.004104812,0.613115256,0.000782421,0.010023372,0.000000000],[0.074428341,0.036143291,0.008785937,0.003854569,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G978 - C985 cWW 
HairpinNode  | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A979:A984
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.388888889,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[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 A979
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A980
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A981
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.009803922,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.696078431,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.284313725,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009803922,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C982
Interaction  | Interacting Bases [5,5] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A983
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[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 A984
Sequences of instances from HL_42998.2:
> HL_42998.2  5J7L G  978 C  985
GAAACAAC
> HL_42998.2  4WF9 G 1022 C 1029
GAAACAGC
> HL_42998.2  7A0S G  989 C  996
GAAACAAC
> HL_42998.2  9DFE G  978 C  985
GGAACAAC
> HL_42998.2  4V9F G 1076 C 1083
GGAACAAC
> HL_42998.2  8CRE G 1144 C 1151
GGAUGAAC
> HL_42998.2  8P9A G 1148 C 1155
GGAUGAAC