Alignment of J3_35321.1 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
3
I

4
4

2
5
5
I

6
6

3
7
7
I

8
8

4
9
9
I

10
10

5
11
11
I

12
14

6
13
14
I

14
15


15
14
I

16
14

7
17
13
I

18
17

8
19
17
I

20
18


21
17
I

22
17

9
23
3
I

24
2

10
25
2
I

26
2

11
27
2
I

28
2

12
29
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
J3_35321.1_Instance_1 J3_35321.1,J3_5TBW_006,C1092_G1066CAUUUGAUUAGAAG
J3_35321.1_Sequence_1 J3_35321.15TBW_C_1092_G_1066CAUUUGA*UU*AGAAGtrue100000.00

Conserved interactions between motif group positions in J3_35321.1:
1 12 cWW 
2 11 s53 
4 5 s53 
5 10 s53 
6 7 cWW 
6 8 s55 
6 9 s53 
7 8 s35 
8 9 cWW 
10 12 cSS 
11 12 s55
JAR3D SCFG/MRF model for J3_35321.1:
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 [12] // Initial node
ClusterNode  | Deletion Probability [0.0000000000030508] | Num Left Bases [1] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.253583698626770] // Cluster node 5TBW|1|1|C|1092:5TBW|1|1|C|1092 and 5TBW|1|1|G|1063:5TBW|1|1|G|1066
Interaction  | Interacting Bases [1,4] | 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 5TBW|1|1|C|1092 - 5TBW|1|1|G|1066 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.028971070,0.034088743,0.032013412,0.040390028,0.000000000],[0.030365737,0.036156702,0.014349547,0.205058125,0.000000000],[0.035569700,0.014075744,0.382324302,0.035593600,0.000000000],[0.018362595,0.034154598,0.032166021,0.026360075,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5TBW|1|1|G|1063 - 5TBW|1|1|G|1066 cSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 5TBW|1|1|A|1064
Insertion    | Location [3] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 11, position 3 in cluster node
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 [2] | Right Index [9] // Initial node 5TBW|1|1|A|1093 - 5TBW|1|1|A|1062 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 5TBW|1|1|U|987
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 [3] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 5TBW|1|1|A|1062
InitialNode  | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left for 5TBW|1|1|G|1063
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 [5] | Right Index [9] // 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 [5] | Right Index [9] // Fixed node on left for 5TBW|1|1|A|1064
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 [6] | Right Index [9] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [6] | Right Index [9] // Junction node A1098 - A1062 ID J3922
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 [6] | Right Index [7] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[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 [6] | Right Index [7] // Basepair A1098 - U986 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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 [8] | Right Index [9] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[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 [8] | Right Index [9] // Basepair U987 - A1062 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_35321.1:
> J3_35321.1  5TBW C 1092 G 1066
CAUUUGA*UU*AGAAG