Alignment of HL_02581.1 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
3
I

6
4

3
7
4
I

8
5

4
9
5
I

10
6

5
11
6
I

12
6

6
13
6
I

14
6

7
15
5
I

16
5

8
17
4
I

18
4

9
19
3
I

20
3

10
21
2
I

22
2

11
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_02581.1_Instance_1 HL_02581.1,HL_1WZ2_005,C912_G926CGAGCCUGGUCAAAG
HL_02581.1_Sequence_1 HL_02581.11WZ2_C912_G926CGAGCCUGGUCAAAGtrue100000.02
HL_02581.1_Instance_2 HL_02581.1,HL_2ZZM_001,C12_G23CAAGCCUGGCCAAAG
HL_02581.1_Sequence_2 HL_02581.12ZZM_C12_G23CAAGCCUGGCCAAAGtrue100000.00

Conserved interactions between motif group positions in HL_02581.1:
1 2 s35 
1 11 cWW 
2 3 s35 
2 10 tSH 
2 11 s55 
3 4 s35 
3 9 cWS 
3 10 s55 
4 5 s35 
4 8 tSW 
6 7 s33 
10 11 s35 
6 5 7BPh
10 2 6BR
JAR3D SCFG/MRF model for HL_02581.1:
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 [11] // 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 [11] // Basepair C912 - G926 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.154632842,0.070001426,0.001561279,0.008583379,0.000000000],[0.142561388,0.094674247,0.001561279,0.001561279,0.000000000],[0.151162568,0.001561279,0.010992220,0.076743448,0.000000000],[0.142578616,0.138702190,0.001561279,0.001561279,0.000000000],[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 [2] | Right Index [10] // Basepair G913 - A925 tSH 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.239509115,0.202271002,0.213757220,0.206617428,0.000000000],[0.016161407,0.013181506,0.002199013,0.013377455,0.000000000],[0.021852929,0.002199013,0.028008345,0.010460203,0.000000000],[0.007850573,0.008281367,0.006553550,0.007719875,0.000000000],[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 [3] | Right Index [9] // Basepair A914 - A924 cWS 
BasepairNode | Deletion Probability [0.0000000000029562] | Pair Probability [[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.135802279,0.007408683,0.000000000],[0.007408683,0.760476157,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[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 [0.000000000,0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.062500000,0.187500000,0.562500000,0.187500000,0.000000000] | Left Index [4] | Right Index [8] // Basepair G915 - C922 tSW 
HairpinNode  | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node C916:U918
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 C916
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.906250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C917
Interaction  | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U918
Sequences of instances from HL_02581.1:
> HL_02581.1  1WZ2 C  912 G  926
CGAGCCUGGUCAAAG
> HL_02581.1  2ZZM C   12 G   23
CAAGCCUGGCCAAAG