Alignment of HL_93616.2 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
4
I

8
4

4
9
4
I

10
4

5
11
4
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
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Full
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Alignment
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HL_93616.2_Instance_1 HL_93616.2,HL_5E81_211,C13_G23CAGCCCGGUAG
HL_93616.2_Sequence_1 HL_93616.25E81_C13_G23CAGCCCGGUAGtrue93001.47
HL_93616.2_Instance_2 HL_93616.2,HL_9DFC_103,C13_G22CAGCCUGGUAG
HL_93616.2_Sequence_2 HL_93616.29DFC_C13_G22CAGCCUGGUAGtrue100000.00
HL_93616.2_Instance_3 HL_93616.2,HL_6CFJ_106,C13_G22CAGCCUGGUAG
HL_93616.2_Sequence_3 HL_93616.26CFJ_C13_G22CAGCCUGGUAGtrue100000.00
HL_93616.2_Instance_4 HL_93616.2,HL_4V9Q_213,C13_G22CAGCCUGGUAG
HL_93616.2_Sequence_4 HL_93616.24V9Q_C13_G22CAGCCUGGUAGtrue100000.00
HL_93616.2_Instance_5 HL_93616.2,HL_1J1U_001,C513_G523CAGCCUGGUAG
HL_93616.2_Sequence_5 HL_93616.21J1U_C513_G523CAGCCUGGUAGtrue100000.00
HL_93616.2_Instance_6 HL_93616.2,HL_4TUE_033,C12_G22CAGCCUGGUAG
HL_93616.2_Sequence_6 HL_93616.24TUE_C12_G22CAGCCUGGUAGtrue100000.00
HL_93616.2_Instance_7 HL_93616.2,HL_2ZUE_001,U913_G922UAGCCAGGACAG
HL_93616.2_Sequence_7 HL_93616.22ZUE_U913_G922UAGCCAGGACAGtrue54009.11
HL_93616.2_Instance_8 HL_93616.2,HL_4WT8_215,C13_G23CAGCCUGGUAG
HL_93616.2_Sequence_8 HL_93616.24WT8_C13_G23CAGCCUGGUAGtrue100000.00

Conserved interactions between motif group positions in HL_93616.2:
1 8 cWW 
2 3 s35 
2 7 cWS 
2 8 s55 
5 6 s33 
4 3 7BPh
JAR3D SCFG/MRF model for HL_93616.2:
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 [0.0000244705618206] | Pair Probability [[0.009208593,0.015783273,0.010745640,0.168677786,0.000000000],[0.052472500,0.011326232,0.242509946,0.013289351,0.000000000],[0.010884288,0.172199894,0.002117259,0.021124324,0.000000000],[0.176582545,0.012713198,0.070413632,0.009951539,0.000000000],[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 C13 - G23 cWW 
BasepairNode | Deletion Probability [0.0000000000015891] | Pair Probability [[0.281758609,0.191033724,0.201881819,0.195138682,0.000000000],[0.015263551,0.012449200,0.002076845,0.012634263,0.000000000],[0.020638877,0.002076845,0.026452326,0.009879081,0.000000000],[0.007414430,0.007821291,0.006189464,0.007290993,0.000000000],[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 [0.000000000,0.000000000,0.005399568,0.864702252,0.128818266,0.001041345,0.000038568] | Right Letter Distribution [0.055555556,0.055555556,0.611111111,0.277777778,0.000000000] | Left Index [2] | Right Index [7] // Basepair A14 - A22 cWS 
HairpinNode  | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G15:C18
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.050000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.050000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.850000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.008620690,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.974137931,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.008620690,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.008620690,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C16
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.050000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.850000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.050000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C17
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.150000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.150000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.050000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.650000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C18
Sequences of instances from HL_93616.2:
> HL_93616.2  5E81 C   13 G   23
CAGCCCGGUAG
> HL_93616.2  9DFC C   13 G   22
CAGCCUGGUAG
> HL_93616.2  6CFJ C   13 G   22
CAGCCUGGUAG
> HL_93616.2  4V9Q C   13 G   22
CAGCCUGGUAG
> HL_93616.2  1J1U C  513 G  523
CAGCCUGGUAG
> HL_93616.2  4TUE C   12 G   22
CAGCCUGGUAG
> HL_93616.2  2ZUE U  913 G  922
UAGCCAGGACAG
> HL_93616.2  4WT8 C   13 G   23
CAGCCUGGUAG