Alignment of HL_36335.1 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
3

2
5
4
I

6
7

3
7
7
I

8
8

4
9
8
I

10
9

5
11
8
I

12
8

6
13
7
I

14
7

7
15
6
I

16
5

8
17
2
I

18
2

9
19
1
I


In
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region

Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_36335.1_Instance_1 HL_36335.1,HL_5W1H_001,C-19_G-10CAAGAAAGAG
HL_36335.1_Sequence_1 HL_36335.15W1H_C-19_G-10CAAGAAAGAGtrue100000.00
HL_36335.1_Instance_2 HL_36335.1,HL_5WLH_001,C-19_G-10CAAGAAAGAG
HL_36335.1_Sequence_2 HL_36335.15WLH_C-19_G-10CAAGAAAGAGtrue100000.00

Conserved interactions between motif group positions in HL_36335.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 9 s55 
3 4 s35 
3 7 cSS 
4 6 cSS 
5 6 s55 
6 7 s35 
7 8 s35
JAR3D SCFG/MRF model for HL_36335.1:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [9] // Basepair C-19 - G-10 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 5W1H|1|B|A|-18
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // Fixed node on right for 5W1H|1|B|G|-12
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 [3] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.082257101,0.085474491,0.108530030,0.083901141,0.000000000],[0.077064975,0.084007429,0.003447499,0.077365799,0.000000000],[0.078895708,0.003373101,0.007643728,0.077979839,0.000000000],[0.072852721,0.011490248,0.061320564,0.084395624,0.000000000],[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 [3] | Right Index [7] // Basepair A-17 - G-12 cSS 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.082257101,0.077064975,0.078895708,0.072852721,0.000000000],[0.085474491,0.084007429,0.003373101,0.011490248,0.000000000],[0.108530030,0.003447499,0.007643728,0.061320564,0.000000000],[0.083901141,0.077365799,0.077979839,0.084395624,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Left Index [4] | Right Index [6] // Basepair G-16 - A-13 cSS 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A-15:A-15
Interaction  | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A-15
Sequences of instances from HL_36335.1:
> HL_36335.1  5W1H C  -19 G  -10
CAAGAAAGAG
> HL_36335.1  5WLH C  -19 G  -10
CAAGAAAGAG