Alignment of HL_25847.2 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
4
I

6
5

3
7
6
I

8
7

4
9
7
I

10
7

5
11
7
I

12
7

6
13
6
I

14
5

7
15
5
I

16
5

8
17
5
I

18
5

9
19
2
I

20
2

10
21
1
I


In
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Cutoff
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Full
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distance
Interior
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Alignment
score
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HL_25847.2_Instance_1 HL_25847.2,HL_9DFE_046,G1910_C1920GUAACUAUAAC
HL_25847.2_Sequence_1 HL_25847.29DFE_G_1910_C_1920GUAACUAUAACtrue100000.00
HL_25847.2_Instance_2 HL_25847.2,HL_8CRE_047,G2231_C2241GUAACUAUGAC
HL_25847.2_Sequence_2 HL_25847.28CRE_G_2231_C_2241GUAACUAUGACtrue98000.49
HL_25847.2_Instance_3 HL_25847.2,HL_5J7L_181,G1910_C1920GUAACUAUAAC
HL_25847.2_Sequence_3 HL_25847.25J7L_G_1910_C_1920GUAACUAUAACtrue100000.00

Conserved interactions between motif group positions in HL_25847.2:
1 2 s35 
1 10 cWW 
2 8 s33 
3 7 tHW 
3 8 s55 
3 9 s55 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 cSH 
9 10 s35 
8 3 6BPh
10 9 7BPh
2 8 6BR
JAR3D SCFG/MRF model for HL_25847.2:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[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 [10] // Basepair G1910 - C1920 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.029411765,0.029411765,0.029411765,0.911764706,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 9DFE|1|1A|PSU|1911
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [3] | Right Index [9] | Norm Constant [1.000000000000000] // Cluster node 9DFE|1|1A|A|1912:9DFE|1|1A|A|1912 and 9DFE|1|1A|PSU|1917:9DFE|1|1A|A|1919
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.018593320,0.041379046,0.004114731,0.440599350,0.000000000],[0.004114731,0.331568716,0.009863283,0.004114731,0.000000000],[0.019312206,0.004114731,0.031292185,0.023873178,0.000000000],[0.004114731,0.004114731,0.018300908,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|1912 - 9DFE|1|1A|PSU|1917 tHW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.239970025,0.200720039,0.010906733,0.041939827,0.000000000],[0.030483930,0.041095973,0.000506089,0.020412171,0.000000000],[0.147004449,0.001663893,0.042884793,0.120378914,0.000000000],[0.031778319,0.028747204,0.000506089,0.041001552,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|1918 - 9DFE|1|1A|A|1919 cSH 
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C1914:A1916
Interaction  | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1914
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1915
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[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 A1916
Sequences of instances from HL_25847.2:
> HL_25847.2  9DFE G 1910 C 1920
GUAACUAUAAC
> HL_25847.2  8CRE G 2231 C 2241
GUAACUAUGAC
> HL_25847.2  5J7L G 1910 C 1920
GUAACUAUAAC