Alignment of IL_91698.1 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
4

3
7
5
I

8
6

4
9
7
I

10
8

5
11
9
I

12
10

6
13
11
I

14
18

7
15
18
I

16
19

8
17
20
I

18
23

9
19
23
I

20
24


21
23
I

22
23

10
23
22
I

24
21

11
25
18
I

26
18

12
27
17
I

28
16

13
29
15
I

30
14

14
31
13
I

32
12

15
33
3
I

34
3

16
35
2
I

36
2

17
37
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_91698.1_Instance_1 IL_91698.1,IL_8P9A_448,U1519_A1487UUGUGAAACGCCAGCGA
IL_91698.1_Sequence_1 IL_91698.18P9A_U_1519_A_1487UUGUGAAAC*GCCAGCGAtrue100000.00
IL_91698.1_Instance_2 IL_91698.1,IL_8CRE_462,U1506_A1473UUGUGAAACGCCAGCGA
IL_91698.1_Sequence_2 IL_91698.18CRE_U_1506_A_1473UUGUGAAAC*GCCAGCGAtrue100000.00

Conserved interactions between motif group positions in IL_91698.1:
1 2 s33 
1 17 cWW 
2 4 s55 
2 16 tWW 
3 5 s33 
6 7 s35 
6 13 s55 
7 8 s35 
7 12 tHW 
8 9 s35 
9 10 cWW 
10 11 s35 
13 14 s35 
14 15 s35 
15 16 s35 
16 17 s35 
5 3 6BPh
5 5 2BPh
12 6 7BPh
11 10 7BPh
3 12 6BPh
3 13 2BPh
1 2 7BR
JAR3D SCFG/MRF model for IL_91698.1:
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 [17] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.004231446,0.008217507,0.004641625,0.091951699,0.000000000],[0.010324811,0.004604899,0.092261070,0.005173142,0.000000000],[0.004650678,0.091080305,0.000957473,0.010794867,0.000000000],[0.498344450,0.024295870,0.124808872,0.023661283,0.000000000],[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 [17] // Basepair U1519 - A1487 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.016132647,0.013222764,0.002925794,0.014423455,0.000000000],[0.268574183,0.013818458,0.012328290,0.013607089,0.000000000],[0.002925794,0.009504076,0.025714781,0.013537368,0.000000000],[0.234369790,0.014144852,0.312187293,0.032583365,0.000000000],[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 [2] | Right Index [16] // Basepair U1520 - G1486 tWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.005000000,0.005000000,0.985000000,0.005000000,0.000000000] | Position [1] | Left Index [3] | Right Index [15] // Fixed node on left for 8P9A|1|sR|C|1482
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 [15] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [4] | Right Index [15] // Fixed node on left for 8P9A|1|sR|A|1483
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 [15] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.005000000,0.005000000,0.985000000,0.005000000,0.000000000] | Position [1] | Left Index [5] | Right Index [15] // Fixed node on left for 8P9A|1|sR|G|1484
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 [15] // 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 [6] | Right Index [15] // Fixed node on left for 8P9A|1|sR|C|1485
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 [15] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [7] | Right Index [15] // Fixed node on right for 8P9A|1|sR|A|1525
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] | Right Index [14] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [7] | Right Index [14] // Fixed node on right for 8P9A|1|sR|A|1524
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [7] | Right Index [13] // Fixed node on right for 8P9A|1|sR|G|1523
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009033872,0.758410498,0.001055432,0.010613763,0.000000000],[0.001055432,0.053826541,0.003684816,0.001055432,0.000000000],[0.030192645,0.007388027,0.009491031,0.004745246,0.000000000],[0.001055432,0.007388027,0.009728762,0.091275044,0.000000000],[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 [7] | Right Index [12] // Basepair A1525 - C1482 tHW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [8] | Right Index [11] // Fixed node on left for 8P9A|1|sR|A|1487
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 [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.906250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [9] | Right Index [11] // Fixed node on right for 8P9A|1|sR|G|1521
InitialNode  | Left Length Distribution [1.000000000] | 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 [9] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 [9] | Right Index [10] // Basepair C1527 - G1480 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 IL_91698.1:
> IL_91698.1  8P9A U 1519 A 1487
UUGUGAAAC*GCCAGCGA
> IL_91698.1  8CRE U 1506 A 1473
UUGUGAAAC*GCCAGCGA