Alignment of HL_81327.2 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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distance

Alignment
score
deficit
HL_81327.2_Instance_1 HL_81327.2_HL_4V90_032_C13_G22CAGCCGGUAG
HL_81327.2_Sequence_1 HL_81327.2_HL_4V90_032_C13_G22CAGCCGGUAGtrue81003.00
HL_81327.2_Instance_2 HL_81327.2_HL_6JXM_001_C13_G21CAGUGGUAG
HL_81327.2_Sequence_2 HL_81327.2_HL_6JXM_001_C13_G21CAGUGGUAGtrue100000.00
HL_81327.2_Instance_3 HL_81327.2_HL_4V9K_033_C13_G22CAGUUGGUUAG
HL_81327.2_Sequence_3 HL_81327.2_HL_4V9K_033_C13_G22CAGUUGGUUAGtrue89001.64

Conserved interactions between motif group positions in HL_81327.2:
1 5 cWW 
2 3 s35 
2 4 cWS 
2 5 s55 
JAR3D SCFG/MRF model for HL_81327.2:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Initial node C13 - G22 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair C13 - G22 cWW 
BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.282754783,0.190768767,0.201601816,0.194868032,0.000000000],[0.015242381,0.012431933,0.002073965,0.012616740,0.000000000],[0.020610252,0.002073965,0.026415638,0.009865379,0.000000000],[0.007404147,0.007810443,0.006180879,0.007280880,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.000000000,0.005372012,0.327692721,0.333064733,0.327961322,0.005640612,0.000268601] | Right Letter Distribution [0.029411765,0.147058824,0.382352941,0.441176471,0.000000000] | Left Index [2] | Right Index [4] // Basepair A14 - A21 cWS 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G15:G15
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Sequences of instances from HL_81327.2:
> HL_81327.2 HL_4V90_032 C   13 G   22
CAGCCGGUAG
> HL_81327.2 HL_6JXM_001 C   13 G   21
CAGUGGUAG
> HL_81327.2 HL_4V9K_033 C   13 G   22
CAGUUGGUUAG