Alignment of HL_18565.1 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
6

3
7
6
I

8
7

4
9
6
I

10
6

5
11
5
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
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Alignment
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HL_18565.1_Instance_1 HL_18565.1,HL_2ZZN_005,A31_U39ACUGCAGAU
HL_18565.1_Sequence_1 HL_18565.12ZZN_A31_U39ACUGCAGAUtrue97000.53
HL_18565.1_Instance_2 HL_18565.1,HL_5WT1_002,A31_U39ACUGAAGAU
HL_18565.1_Sequence_2 HL_18565.15WT1_A31_U39ACUGAAGAUtrue100000.00

Conserved interactions between motif group positions in HL_18565.1:
1 2 s35 
1 8 cWW 
2 7 cWW 
3 5 cSH 
4 5 s35 
5 6 s35 
6 7 perp 
7 8 s35 
6 4 7BPh
JAR3D SCFG/MRF model for HL_18565.1:
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 [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[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 A31 - U39 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.010153793,0.013295259,0.012926971,0.028012001,0.000000000],[0.435119769,0.037265996,0.031668407,0.014435104,0.000000000],[0.013237803,0.026709543,0.003263854,0.013805080,0.000000000],[0.035195420,0.013154930,0.298667921,0.013088150,0.000000000],[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 [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair C32 - A38 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right for 2ZZN|1|D|A|36
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 [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.082442164,0.088350897,0.007680972,0.084139219,0.000000000],[0.084342963,0.086292904,0.000981194,0.011079913,0.000000000],[0.012396638,0.000981194,0.089503806,0.079842104,0.000000000],[0.183130872,0.107923341,0.000981194,0.079930624,0.000000000],[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 [5] // Basepair U33 - C35 cSH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G34:G34
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[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 G34
Sequences of instances from HL_18565.1:
> HL_18565.1  2ZZN A   31 U   39
ACUGCAGAU
> HL_18565.1  5WT1 A   31 U   39
ACUGAAGAU