Alignment of HL_73183.1 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
5
I

8
6

4
9
6
I

10
6

5
11
6
I

12
6

6
13
6
I

14
6

7
15
6
I

16
6

8
17
6
I

18
6

9
19
6
I

20
6

10
21
5
I

22
4

11
23
4
I

24
4

12
25
3
I

26
3

13
27
2
I

28
2

14
29
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
HL_73183.1_Instance_1 HL_73183.1,HL_6ZDU_002,C1297_G1314CGAAAAAAUUGGAAGUAG
HL_73183.1_Sequence_1 HL_73183.16ZDU_C_1297_G_1314CGAAAAAAUUGGAAGUAGtrue93001.27
HL_73183.1_Instance_2 HL_73183.1,HL_3IGI_002,U47_A61UGAAGGCAGAAGUAA
HL_73183.1_Sequence_2 HL_73183.13IGI_U47_A61UGAAGGCAGAAGUAAtrue100000.00

Conserved interactions between motif group positions in HL_73183.1:
1 2 s35 
1 14 cWW 
2 11 s33 
2 12 s33 
2 13 tSH 
2 14 s55 
3 12 tHW 
3 13 s55 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
8 11 s35 
9 10 s35 
10 11 s35 
10 12 s35 
11 12 cSH 
12 13 s35 
13 14 s35 
11 3 6BPh
2 12 6BPh
13 2 6BR
JAR3D SCFG/MRF model for HL_73183.1:
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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009285457,0.017323068,0.010436779,0.197555258,0.000000000],[0.021160175,0.009772202,0.212782490,0.012417770,0.000000000],[0.010508004,0.198766713,0.002067002,0.023256875,0.000000000],[0.212699647,0.011830790,0.040032900,0.010104868,0.000000000],[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 [14] // Basepair C1297 - G1314 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.046260217,0.000524565,0.002472278,0.000000000],[0.044022640,0.046153098,0.000524565,0.000524565,0.000000000],[0.386803555,0.003671957,0.017951032,0.311661837,0.000000000],[0.048778633,0.045903932,0.000524565,0.000524565,0.000000000],[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 [2] | Right Index [13] // Basepair G1298 - A1313 tSH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [12] | Norm Constant [0.284598840458439] // Cluster node 6ZDU|1|C|A|1299:6ZDU|1|C|A|1299 and 6ZDU|1|C|G|1311:6ZDU|1|C|U|1312
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.018775607,0.041784723,0.004155072,0.435115030,0.000000000],[0.004155072,0.334819390,0.009959982,0.004155072,0.000000000],[0.019501541,0.004155072,0.031598971,0.024107229,0.000000000],[0.004155072,0.004155072,0.018480329,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6ZDU|1|C|A|1299 - 6ZDU|1|C|U|1312 tHW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.028278186,0.028814174,0.001584293,0.028159695,0.000000000],[0.021111513,0.031815420,0.000350789,0.028218728,0.000000000],[0.172946967,0.002455525,0.210965819,0.354286885,0.000000000],[0.028716948,0.028544556,0.000350789,0.033399713,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6ZDU|1|C|G|1311 - 6ZDU|1|C|U|1312 cSH 
InitialNode  | Left Length Distribution [0.011890606,0.475624257,0.023781213,0.476218787,0.011890606,0.000594530] | Left Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Cluster
HairpinNode  | Num Bases [7] | Left Index [4] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node A1303:A1310
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 A1303
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 A1304
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1305
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1306
Interaction  | Interacting Bases [5,5] | 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 G1307
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[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 A1309
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[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 A1310
Insertion    | Location [5] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 8, position 5
Sequences of instances from HL_73183.1:
> HL_73183.1  6ZDU C 1297 G 1314
CGAAAAAAUUGGAAGUAG
> HL_73183.1  3IGI U   47 A   61
UGAAGGCAGAAGUAA