Alignment of HL_86012.1 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
7

2
5
7
I

6
8

3
7
8
I

8
8

4
9
7
I

10
7

5
11
6
I

12
5

6
13
4
I

14
3

7
15
2
I

16
2

8
17
1
I


In
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Interior
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Alignment
score
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HL_86012.1_Instance_1 HL_86012.1,HL_1ZL3_001,G408_C416GUUCGAUCC
HL_86012.1_Sequence_1 HL_86012.11ZL3_G408_C416GUUCGAUCCtrue100000.00
HL_86012.1_Instance_2 HL_86012.1,HL_1R3E_001,G408_C416GUUCGAUCC
HL_86012.1_Sequence_2 HL_86012.11R3E_G408_C416GUUCGAUCCtrue100000.00

Conserved interactions between motif group positions in HL_86012.1:
1 2 s35 
1 8 cWW 
2 5 tWH 
3 4 s33 
5 7 perp 
5 8 s35 
6 7 s35 
7 5 7BPh
8 7 7BPh
4 3 2BR
JAR3D SCFG/MRF model for HL_86012.1:
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 [0.0000229437914523] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G408 - C416 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.906250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [2] | Right Index [7] // Fixed node on right for 1ZL3|1|B|U|414
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [2] | Right Index [6] // Fixed node on right for 1ZL3|1|B|A|413
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair U409 - A413 tWH 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node C411:G412
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C411
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.875000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G412
Sequences of instances from HL_86012.1:
> HL_86012.1  1ZL3 G  408 C  416
GUUCGAUCC
> HL_86012.1  1R3E G  408 C  416
GUUCGAUCC