Alignment of IL_15218.1 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
10
I

12
11

6
13
12
I

14
13

7
15
14
I

16
15

8
17
16
I

18
17

9
19
18
I

20
19

10
21
20
I

22
21

11
23
21
I

24
22


25
21
I

26
21

12
27
2
I

28
2

13
29
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_15218.1_Instance_1 IL_15218.1,IL_7QR3_001,C7_G30CACAGCAGAAGCG
IL_15218.1_Sequence_1 IL_15218.17QR3_C7_G30CACAGCAGAAG*CGtrue100000.00
IL_15218.1_Instance_2 IL_15218.1,IL_4PR6_001,C107_G131CAUGGUCCCAGCG
IL_15218.1_Sequence_2 IL_15218.14PR6_C107_G131CAUGGUCCCAG*CGtrue100000.00

Conserved interactions between motif group positions in IL_15218.1:
1 2 s35 
1 13 cWW 
2 3 s35 
2 13 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
11 12 cWW
JAR3D SCFG/MRF model for IL_15218.1:
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 [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C7 - G30 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 7QR3|1|C|A|8
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 7QR3|1|C|C|9
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left for 7QR3|1|C|A|10
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [12] // Fixed node on left for 7QR3|1|C|G|11
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [6] | Right Index [12] // Fixed node on left for 7QR3|1|C|C|12
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [7] | Right Index [12] // Fixed node on left for 7QR3|1|C|A|13
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.375000000,0.125000000,0.000000000] | Position [1] | Left Index [8] | Right Index [12] // Fixed node on left for 7QR3|1|C|G|14
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [9] | Right Index [12] // Fixed node on left for 7QR3|1|C|A|15
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [10] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [10] | Right Index [12] // Fixed node on left for 7QR3|1|C|A|16
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [11] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [12] // Basepair G17 - C29 cWW 
HairpinNode  | Num Bases [1] | Left Index [12] | Right Index [12] | 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 IL_15218.1:
> IL_15218.1  7QR3 C    7 G   30
CACAGCAGAAG*CG
> IL_15218.1  4PR6 C  107 G  131
CAUGGUCCCAG*CG