Alignment of HL_19958.1 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
5

5
11
4
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_19958.1_Instance_1 HL_19958.1_HL_4QEI_004_G12_C23GUAGUGGUAUC
HL_19958.1_Sequence_1 HL_19958.1_HL_4QEI_004_G12_C23GUAGUGGUAUCtrue100000.00
HL_19958.1_Instance_2 HL_19958.1_HL_4QEI_001_G12_C23GUAGUGGUAUC
HL_19958.1_Sequence_2 HL_19958.1_HL_4QEI_001_G12_C23GUAGUGGUAUCtrue100000.00
HL_19958.1_Instance_3 HL_19958.1_HL_5E6M_001_G12_C23GUAGUGGUAUC
HL_19958.1_Sequence_3 HL_19958.1_HL_5E6M_001_G12_C23GUAGUGGUAUCtrue100000.00
HL_19958.1_Instance_4 HL_19958.1_HL_2DU3_001_A912_U922AGAGGGGCUUU
HL_19958.1_Sequence_4 HL_19958.1_HL_2DU3_001_A912_U922AGAGGGGCUUUtrue90001.75
HL_19958.1_Instance_5 HL_19958.1_HL_2DU3_004_A912_U922AGAGGGGCUUU
HL_19958.1_Sequence_5 HL_19958.1_HL_2DU3_004_A912_U922AGAGGGGCUUUtrue90001.75

Conserved interactions between motif group positions in HL_19958.1:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 cWW 
3 4 s35 
3 6 cWS 
3 7 s55 
4 5 s35 
7 8 s35 
JAR3D SCFG/MRF model for HL_19958.1:
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 [8] // Initial node G12 - C23 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009280432,0.020368229,0.010312873,0.215702181,0.000000000],[0.016772457,0.009285906,0.193782875,0.011767824,0.000000000],[0.010233627,0.226772067,0.002010885,0.036277626,0.000000000],[0.192008674,0.012321377,0.022616385,0.010486579,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G12 - C23 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014050246,0.257698632,0.012544499,0.021909755,0.000000000],[0.015528856,0.016743948,0.018727607,0.013770962,0.000000000],[0.012282488,0.019077752,0.003872504,0.128043403,0.000000000],[0.019139631,0.014913942,0.015873928,0.415821848,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U13 - U22 cWW 
BasepairNode | Deletion Probability [0.0000000000030757] | Pair Probability [[0.228838658,0.184211091,0.194671754,0.266740872,0.000000000],[0.014718424,0.012004586,0.002002672,0.012183040,0.000000000],[0.019901775,0.002002672,0.025507600,0.009526256,0.000000000],[0.007149629,0.007541959,0.005968411,0.007030600,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.029411765,0.147058824,0.617647059,0.205882353,0.000000000] | Left Index [3] | Right Index [6] // Basepair A14 - A21 cWS 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G15:U16
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.785714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.357142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U16
Sequences of instances from HL_19958.1:
> HL_19958.1 HL_4QEI_004 G   12 C   23
GUAGUGGUAUC
> HL_19958.1 HL_4QEI_001 G   12 C   23
GUAGUGGUAUC
> HL_19958.1 HL_5E6M_001 G   12 C   23
GUAGUGGUAUC
> HL_19958.1 HL_2DU3_001 A  912 U  922
AGAGGGGCUUU
> HL_19958.1 HL_2DU3_004 A  912 U  922
AGAGGGGCUUU