Alignment of J3_99170.1 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
3

3
7
3
I

8
3

4
9
4
I

10
5

5
11
6
I

12
9

6
13
9
I

14
10


15
9
I

16
9

7
17
8
I

18
12

8
19
13
I

20
14

9
21
14
I

22
15


23
14
I

24
14

10
25
4
I

26
3

11
27
3
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_99170.1_Instance_1 J3_99170.1,J3_5TBW_008,U1479_A1874UGAAGUGCAAUCUA
J3_99170.1_Sequence_1 J3_99170.15TBW_U_1479_A_1874UGAAGUG*CAA*UCUAtrue100000.00

Conserved interactions between motif group positions in J3_99170.1:
1 13 cWW 
2 11 s33 
2 12 tSH 
3 4 s55 
3 9 s35 
3 11 tHW 
3 12 s55 
4 12 tWW 
4 13 s35 
6 7 cWW 
7 8 s35 
9 10 cWW 
9 11 s55 
11 12 s35 
12 13 s35 
9 3 7BPh
2 11 6BPh
JAR3D SCFG/MRF model for J3_99170.1:
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 [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[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 [0.989901010,0.009999000,0.000099990] | 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 U1479 - A1874 cWW 
ClusterNode  | Deletion Probability [0.000000000000015254027177953870338373321144532320374926368314] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [12] | Norm Constant [0.312390441543080] // Cluster node 5TBW|1|1|G|1480:5TBW|1|1|G|1483 and 5TBW|1|1|C|1872:5TBW|1|1|U|1873
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.031021441,0.372326222,0.003624252,0.036446633,0.000000000],[0.003624252,0.026405017,0.012653299,0.003624252,0.000000000],[0.103678615,0.003624252,0.032591280,0.016294714,0.000000000],[0.003624252,0.003624252,0.033407624,0.313429642,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5TBW|1|1|A|1481 - 5TBW|1|1|C|1872 tHW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.013854278,0.017490019,0.000634771,0.003852439,0.000000000],[0.008036166,0.007901960,0.000634771,0.000634771,0.000000000],[0.377138465,0.004443394,0.031837578,0.454240370,0.000000000],[0.052697754,0.025333725,0.000634771,0.000634771,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5TBW|1|1|G|1480 - 5TBW|1|1|U|1873 tSH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.017035113,0.277461015,0.003022606,0.242124836,0.000000000],[0.013660292,0.014465734,0.009818556,0.014612890,0.000000000],[0.003022606,0.012736220,0.014938620,0.312161581,0.000000000],[0.014900712,0.014057333,0.013985305,0.021996583,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5TBW|1|1|G|1483 - 5TBW|1|1|U|1873 tWW 
Insertion    | Location [2] | 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 3, position 2 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 [5] | Right Index [10] // Initial node 5TBW|1|1|U|1484 - 5TBW|1|1|U|1871 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 5TBW|1|1|G|1483
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 [10] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [6] | Right Index [10] // Junction node G1485 - U1871 ID J7537
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 [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[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 [6] | Right Index [7] // Basepair G1485 - C1857 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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [10] // Initial node 5TBW|1|1|A|1858 - 5TBW|1|1|U|1871 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 5TBW|1|1|C|1857
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 [[0.026235093,0.062205457,0.028019647,0.586764415,0.000000000],[0.007072752,0.003867915,0.078392192,0.004182258,0.000000000],[0.003995015,0.079408468,0.000824091,0.021484428,0.000000000],[0.079142195,0.004452488,0.009291068,0.004662519,0.000000000],[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 A1859 - U1871 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_99170.1:
> J3_99170.1  5TBW U 1479 A 1874
UGAAGUG*CAA*UCUA