Alignment of HL_42733.3 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
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_42733.3_Instance_1 HL_42733.3_HL_4V9F_043_C1705_G1713CGGCGAAAG
HL_42733.3_Sequence_1 HL_42733.3_HL_4V9F_043_C_1705_G_1713CGGCGAAAGtrue92000.86
HL_42733.3_Instance_2 HL_42733.3_HL_5J7L_012_G462_C470GUUAAUACC
HL_42733.3_Sequence_2 HL_42733.3_HL_5J7L_012_G462_C470GUUAAUACCtrue96000.50
HL_42733.3_Instance_3 HL_42733.3_HL_1QTQ_002_A931_U939AUUCUGAUU
HL_42733.3_Sequence_3 HL_42733.3_HL_1QTQ_002_A931_U939AUUCUGAUUtrue100000.00

Conserved interactions between motif group positions in HL_42733.3:
1 2 s35 
1 8 cWW 
2 3 s35 
3 6 tSH 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
JAR3D SCFG/MRF model for HL_42733.3:
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 C1705 - G1713 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009425327,0.019602391,0.010550535,0.209161741,0.000000000],[0.018119710,0.009519290,0.209803050,0.012356683,0.000000000],[0.010544174,0.210633518,0.002053265,0.034146945,0.000000000],[0.196782200,0.012577586,0.024177876,0.010545706,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C1705 - G1713 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.300000000,0.500000000,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.300000000,0.300000000,0.100000000,0.300000000,0.000000000] | 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 [0.993970181,0.005999820,0.000029999] | 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 [0.0000001200211660] | Pair Probability [[0.109940024,0.108141163,0.001268721,0.006109495,0.000000000],[0.110554335,0.109778424,0.001268721,0.001268721,0.000000000],[0.132160344,0.001268721,0.007016842,0.106513064,0.000000000],[0.188046810,0.114127171,0.001268721,0.001268721,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair G1707 - A1711 tSH 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node C1708:G1709
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1708
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1709
Sequences of instances from HL_42733.3:
> HL_42733.3 HL_4V9F_043 C 1705 G 1713
CGGCGAAAG
> HL_42733.3 HL_5J7L_012 G  462 C  470
GUUAAUACC
> HL_42733.3 HL_1QTQ_002 A  931 U  939
AUUCUGAUU