Alignment of J4_57344.1 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
2

2
5
3
I

6
6

3
7
6
I

8
7


9
6
I

10
6

4
11
5
I

12
11

5
13
11
I

14
12


15
11
I

16
11

6
17
10
I

18
14

7
19
15
I

20
16

8
21
17
I

22
18

9
23
18
I

24
19


25
18
I

26
18

10
27
3
I

28
2

11
29
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J4_57344.1_Instance_1 J4_57344.1,J4_5UD5_001,C7_G66CUGCGCAGCGG
J4_57344.1_Sequence_1 J4_57344.15UD5_C7_G66CUG*CG*CAGC*GGtrue100000.00

Conserved interactions between motif group positions in J4_57344.1:
1 2 cSH 
1 9 s35 
1 11 cWW 
2 9 s35 
2 11 tHS 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 cWW 
7 8 s35 
9 10 cWW 
9 11 s55 
10 11 s35
JAR3D SCFG/MRF model for J4_57344.1:
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 [11] // Initial node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [11] | Norm Constant [0.017170344182355] // Cluster node 5UD5|1|C|C|7:5UD5|1|C|U|9 and 5UD5|1|C|G|66:5UD5|1|C|G|66
Interaction  | Interacting Bases [1,3] | 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]] // Cluster Interaction 5UD5|1|C|C|7 - 5UD5|1|C|G|66 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.053818499,0.031217389,0.209290967,0.204710348,0.000000000],[0.067941945,0.030696053,0.002465838,0.098411704,0.000000000],[0.002465838,0.002465838,0.017668093,0.002465838,0.000000000],[0.014965233,0.002465838,0.256484744,0.002465838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5UD5|1|C|U|9 - 5UD5|1|C|G|66 tHS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.012202504,0.014034639,0.007949359,0.143937262,0.000000000],[0.014572214,0.120213100,0.001727817,0.182682671,0.000000000],[0.162968637,0.001727817,0.019991059,0.138991691,0.000000000],[0.014467395,0.019510979,0.001727817,0.143295039,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5UD5|1|C|C|7 - 5UD5|1|C|U|9 cSH 
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 [3] | Right Index [10] // Initial node 5UD5|1|C|G|10 - 5UD5|1|C|G|65 from node 
JunctionNode | Branches [2]  | Left Index [3] | Right Index [10] // Junction node G10 - G65 ID J1492
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 [3] | Right Index [4] // 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 [3] | Right Index [4] // Basepair G10 - C24 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Initial node 5UD5|1|C|G|25 - 5UD5|1|C|G|65 from node 
JunctionNode | Branches [2]  | Left Index [5] | Right Index [10] // Junction node G25 - G65 ID J2575
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 [5] | Right Index [6] // 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 [5] | Right Index [6] // Basepair G25 - C45 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Initial node 5UD5|1|C|A|46 - 5UD5|1|C|G|65 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [7] | Right Index [10] // Fixed node on left for 5UD5|1|C|A|46
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 [8] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 5UD5|1|C|G|47
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 [9] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | 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 C49 - G65 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 J4_57344.1:
> J4_57344.1  5UD5 C    7 G   66
CUG*CG*CAGC*GG