Alignment of J3_32030.1 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
7

2
5
7
I

6
8

3
7
9
I

8
10

4
9
10
I

10
10

5
11
11
I

12
12

6
13
12
I

14
13

7
15
13
I

16
14


17
13
I

18
13

8
19
12
I

20
12

9
21
11
I

22
10

10
23
7
I

24
7

11
25
6
I

26
16

12
27
16
I

28
17


29
16
I

30
16

13
31
4
I

32
3

14
33
2
I

34
2

15
35
1
I


In
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Alignment
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J3_32030.1_Instance_1 J3_32030.1,J3_3NPQ_001,C13_G48CUGCAAGCCCAGCGG
J3_32030.1_Sequence_1 J3_32030.13NPQ_C13_G48CUGCAAG*CCCAG*CGGtrue100000.00

Conserved interactions between motif group positions in J3_32030.1:
1 2 s35 
1 15 cWW 
2 3 s35 
2 11 tWH 
2 15 s55 
3 10 s33 
3 11 s55 
4 5 s35 
4 10 tHS 
5 6 s35 
5 10 tHS 
6 7 s35 
6 9 bif 
7 8 cWW 
8 9 s35 
9 10 s35 
11 15 s35 
12 13 cWW 
12 14 s55 
3 11 6BPh
14 12 2BPh
4 3 7BR
JAR3D SCFG/MRF model for J3_32030.1:
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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair C13 - G48 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Position [2] | Left Index [2] | Right Index [14] // Fixed node on right for 3NPQ|1|A|G|47
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [2] | Right Index [13] // Junction node U14 - C46 ID J8491
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair U14 - A29 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 3NPQ|1|A|G|15
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [4] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.269722604570407] // Cluster node 3NPQ|1|A|C|16:3NPQ|1|A|A|17 and 3NPQ|1|A|C|28:3NPQ|1|A|C|28
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.023251435,0.040958789,0.051504982,0.049789019,0.000000000],[0.262926339,0.302597773,0.002926968,0.250823439,0.000000000],[0.000585394,0.000585394,0.002570719,0.000585394,0.000000000],[0.002436280,0.000585394,0.007287290,0.000585394,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NPQ|1|A|C|16 - 3NPQ|1|A|C|28 tHS 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.166739042,0.181862370,0.144313661,0.155443097,0.000000000],[0.021588854,0.120317856,0.001719614,0.157162461,0.000000000],[0.001719614,0.001719614,0.011932323,0.001719614,0.000000000],[0.008552422,0.001719614,0.021770231,0.001719614,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NPQ|1|A|A|17 - 3NPQ|1|A|C|28 tHS 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.028776211,0.712040258,0.007021393,0.007021393,0.000000000],[0.032326394,0.082230039,0.007021393,0.007021393,0.000000000],[0.007021393,0.007021393,0.029462996,0.007021393,0.000000000],[0.007021393,0.007021393,0.044950176,0.007021393,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A18 - C27 bif 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair G19 - C26 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [12] | Right Index [13] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [13] // Basepair G30 - C46 cWW 
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from J3_32030.1:
> J3_32030.1  3NPQ C   13 G   48
CUGCAAG*CCCAG*CGG