Alignment of IL_76095.3 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
4
I

8
7

4
9
7
I

10
8

5
11
8
I

12
9

6
13
9
I

14
10

7
15
11
I

16
12

8
17
12
I

18
13

9
19
13
I

20
14


21
13
I

22
13

10
23
12
I

24
12

11
25
9
I

26
9

12
27
8
I

28
8

13
29
7
I

30
7

14
31
6
I

32
5

15
33
4
I

34
4

16
35
3
I

36
3

17
37
2
I

38
2

18
39
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_76095.3_Instance_1 IL_76095.3_IL_1M5O_005_G19_C64GAGAAACACGGUAUAUUACC
IL_76095.3_Sequence_1 IL_76095.3_IL_1M5O_005_G19_C64GAGAAACAC*GGUAUAUUACCtrue100000.00
IL_76095.3_Instance_2 IL_76095.3_IL_2P7D_001_G19_C45GAGAAACACGGUACAUUACC
IL_76095.3_Sequence_2 IL_76095.3_IL_2P7D_001_G19_C45GAGAAACAC*GGUACAUUACCtrue100000.00

Conserved interactions between motif group positions in IL_76095.3:
1 2 s35 
1 18 cWW 
2 3 s35 
2 17 cWW 
3 14 s33 
3 16 tSH 
4 5 s35 
4 14 tHW 
4 16 s55 
5 6 s35 
5 13 tHW 
5 15 perp 
6 7 s35 
6 12 tWH 
7 8 s35 
8 9 s35 
8 11 cWW 
9 10 cWW 
10 11 s35 
12 13 s35 
13 14 s35 
14 15 perp 
16 17 s35 
17 18 s35 
17 16 7BPh
16 3 6BR
3 14 6BR
JAR3D SCFG/MRF model for IL_76095.3:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [18] // Initial node G19 - C64 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[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 [18] // Basepair G19 - C64 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.004239289,0.704559841,0.003968692,0.011130938,0.000000000],[0.003985917,0.023716009,0.007830734,0.003917236,0.000000000],[0.003875504,0.066182996,0.000978503,0.087912340,0.000000000],[0.009148129,0.030421125,0.004101169,0.034031578,0.000000000],[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 [17] // Basepair A20 - C63 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.054858579,0.063944697,0.000660976,0.003147483,0.000000000],[0.055346656,0.058011367,0.000660976,0.000660976,0.000000000],[0.350095800,0.003304880,0.016011447,0.274899622,0.000000000],[0.059629333,0.057445257,0.000660976,0.000660976,0.000000000],[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 [3] | Right Index [16] // Basepair G21 - A62 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [4] | Right Index [15] // Fixed node on right
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 [4] | Right Index [14] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.025971800,0.054103855,0.005446896,0.564297448,0.000000000],[0.005446896,0.045222361,0.005446896,0.005446896,0.000000000],[0.026718220,0.036155648,0.063745789,0.067195854,0.000000000],[0.005446896,0.005446896,0.025408179,0.058499471,0.000000000],[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 [4] | Right Index [14] // Basepair A22 - U60 tHW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.418144609,0.031463906,0.003985368,0.019002964,0.000000000],[0.003985368,0.014640658,0.003985368,0.003985368,0.000000000],[0.341751342,0.022813077,0.049366656,0.023593614,0.000000000],[0.003985368,0.003985368,0.035560217,0.019750751,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Left Index [5] | Right Index [13] // Basepair A23 - A59 tHW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.418144609,0.003985368,0.341751342,0.003985368,0.000000000],[0.031463906,0.014640658,0.022813077,0.003985368,0.000000000],[0.003985368,0.003985368,0.049366656,0.035560217,0.000000000],[0.019002964,0.003985368,0.023593614,0.019750751,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [6] | Right Index [12] // Basepair A24 - A57 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [7] | Right Index [11] // Fixed node on left
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 [11] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.194909758,0.012133405,0.318763646,0.013661711,0.000000000],[0.011848504,0.004569762,0.016221879,0.034517612,0.000000000],[0.287416726,0.016428681,0.002991558,0.013487720,0.000000000],[0.013638432,0.036717533,0.013189215,0.009503858,0.000000000],[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 [8] | Right Index [11] // Basepair A26 - G55 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 C27 - G54 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_76095.3:
> IL_76095.3 IL_1M5O_005 G   19 C   64
GAGAAACAC*GGUAUAUUACC
> IL_76095.3 IL_2P7D_001 G   19 C   45
GAGAAACAC*GGUACAUUACC