Alignment of J3_36499.1 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
7

3
7
7
I

8
7

4
9
8
I

10
9


11
8
I

12
7

5
13
7
I

14
7

6
15
7
I

16
7

7
17
7
I

18
7

8
19
6
I

20
13

9
21
13
I

22
14


23
13
I

24
13

10
25
12
I

26
11

11
27
4
I

28
3

12
29
2
I

30
2

13
31
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
J3_36499.1_Instance_1 J3_36499.1,J3_4UYK_001,C10_G135CUAGCGAAGCGUG
J3_36499.1_Sequence_1 J3_36499.14UYK_C10_G135CUAG*CGAAG*CGUGtrue100000.00

Conserved interactions between motif group positions in J3_36499.1:
1 2 s35 
1 13 cWW 
2 3 s35 
2 6 s33 
2 7 tWH 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
4 8 tSS 
5 6 s35 
7 13 s35 
8 11 tHS 
9 10 cWW 
9 11 s55 
10 11 s35 
11 12 s35 
1 7 7BPh
3 6 6BR
7 11 2BR
JAR3D SCFG/MRF model for J3_36499.1:
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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003781516,0.006781167,0.004347319,0.078825460,0.000000000],[0.056281056,0.026959555,0.589952696,0.038278585,0.000000000],[0.004396140,0.080523937,0.000828645,0.009304998,0.000000000],[0.079847353,0.005268669,0.010615539,0.004007366,0.000000000],[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 [13] // Basepair C10 - G135 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [12] // Fixed node on right for 4UYK|1|R|U|134
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 [11] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [2] | Right Index [11] // Junction node U11 - G133 ID J1711
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 [8] // Initial node 4UYK|1|R|U|11 - 4UYK|1|R|A|68 from node 
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [3] | Num Right Bases [4] | Left Index [2] | Right Index [8] | Norm Constant [0.256083596003376] // Cluster node 4UYK|1|R|U|11:4UYK|1|R|G|13 and 4UYK|1|R|C|65:4UYK|1|R|A|68
Interaction  | Interacting Bases [3,4] | 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]] // Cluster Interaction 4UYK|1|R|G|13 - 4UYK|1|R|C|65 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.113862076,0.114707989,0.146584821,0.127100484,0.000000000],[0.120538352,0.120259235,0.001366838,0.119609993,0.000000000],[0.001366838,0.001366838,0.006682038,0.001366838,0.000000000],[0.006441913,0.001366838,0.116012068,0.001366838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4UYK|1|R|A|12 - 4UYK|1|R|G|66 tHS 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.032037056,0.001417970,0.006655145,0.001417970,0.000000000],[0.071297801,0.114261312,0.001417970,0.001417970,0.000000000],[0.007089852,0.003398969,0.010783545,0.006306644,0.000000000],[0.718886159,0.001417970,0.008226894,0.013966772,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4UYK|1|R|U|11 - 4UYK|1|R|A|67 tWH 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.021644907,0.017792930,0.020496934,0.013012017,0.000000000],[0.002614097,0.002614097,0.227437495,0.002614097,0.000000000],[0.271310703,0.002614097,0.254121285,0.153270951,0.000000000],[0.002614097,0.002614097,0.002614097,0.002614097,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4UYK|1|R|G|13 - 4UYK|1|R|A|68 tSS 
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 [5] | Right Index [4] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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 [0.222222222,0.222222222,0.333333333,0.222222222,0.000000000] | Left Index [9] | Right Index [11] // Initial node 4UYK|1|R|G|69 - 4UYK|1|R|G|133 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [2] | Left Index [9] | Right Index [11] // Fixed node on right for 4UYK|1|R|G|133
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 [9] | Right Index [10] // New Initial node after Fixed 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 [9] | Right Index [10] // Basepair G69 - C132 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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_36499.1:
> J3_36499.1  4UYK C   10 G  135
CUAG*CGAAG*CGUG