Alignment of HL_64292.1 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
5

2
5
5
I

6
6

3
7
6
I

8
6

4
9
6
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
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_64292.1_Instance_1 HL_64292.1,HL_8P9A_234,G486_U501GGGCCCAUUCGGGUCU
HL_64292.1_Sequence_1 HL_64292.18P9A_G486_U501GGGCCCAUUCGGGUCUtrue100000.00
HL_64292.1_Instance_2 HL_64292.1,HL_2ANN_001,C5_G21CGGAUCAGUCACCCAAG
HL_64292.1_Sequence_2 HL_64292.12ANN_C5_G21CGGAUCAGUCACCCAAGtrue83002.75

Conserved interactions between motif group positions in HL_64292.1:
1 2 perp 
1 10 cWW 
2 6 perp 
2 7 s33 
2 8 tSH 
3 4 s35 
3 7 s55 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35
JAR3D SCFG/MRF model for HL_64292.1:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.012688202,0.156994168,0.012640552,0.141686075,0.000000000],[0.016999579,0.011251064,0.132507556,0.014097797,0.000000000],[0.012548748,0.122317850,0.002667073,0.183756588,0.000000000],[0.118972395,0.014510822,0.020584598,0.025776931,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | 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 [10] // Basepair G486 - U501 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right for 8P9A|1|sR|U|494
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 [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.102496164,0.108506004,0.001230398,0.005798870,0.000000000],[0.103257637,0.108254748,0.001230398,0.001230398,0.000000000],[0.132843734,0.001230398,0.006015026,0.203362022,0.000000000],[0.114413092,0.107670315,0.001230398,0.001230398,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | 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 [8] // Basepair G488 - U499 tSH 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node C490:G498
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C490
Interaction  | Interacting Bases [2,2] | 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 C491
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 G496
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 G497
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 G498
Insertion    | Location [2] | Length Distribution [0.000000000,0.000000000,0.000000000,0.011890606,0.487514863,0.487514863,0.012485137,0.000594530] | Letter Distribution [0.318181818,0.227272727,0.136363636,0.318181818,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_64292.1:
> HL_64292.1  8P9A G  486 U  501
GGGCCCAUUCGGGUCU
> HL_64292.1  2ANN C    5 G   21
CGGAUCAGUCACCCAAG