Alignment of IL_16330.1 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
12

7
15
13
I

16
14

8
17
15
I

18
34

9
19
34
I

20
35

10
21
35
I

22
36

11
23
36
I

24
37


25
36
I

26
36

12
27
35
I

28
35

13
29
34
I

30
34

14
31
33
I

32
32

15
33
31
I

34
30

16
35
29
I

36
28

17
37
27
I

38
26

18
39
25
I

40
24

19
41
23
I

42
22

20
43
21
I

44
20

21
45
19
I

46
18

22
47
17
I

48
16

23
49
3
I

50
3

24
51
2
I

52
2

25
53
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_16330.1_Instance_1 IL_16330.1_IL_3U5H_057_G1194_C1314GACACCACAAAAUGAAAAUGGAUGGCGC
IL_16330.1_Sequence_1 IL_16330.1_IL_3U5H_057_G_1194_C_1314GACACCACAAAA*UGAAAAUGGAUGGCGCtrue100000.00
IL_16330.1_Instance_2 IL_16330.1_IL_4A1B_058_G1221_C1341GAUACCACAAAAUGAAAAUGGAUGGCGC
IL_16330.1_Sequence_2 IL_16330.1_IL_4A1B_058_G_1221_C_1341GAUACCACAAAA*UGAAAAUGGAUGGCGCtrue100000.00

Conserved interactions between motif group positions in IL_16330.1:
1 2 s35 
1 25 cWW 
2 20 s35 
2 24 cWW 
3 4 s35 
4 5 s33 
5 6 s53 
7 8 s35 
8 14 s35 
9 10 s35 
9 13 s33 
9 14 tHH 
10 11 s35 
10 13 tHS 
11 12 cWW 
11 13 s55 
12 13 s35 
13 14 s33 
15 16 s35 
18 19 s35 
21 22 s35 
22 23 s35 
23 24 s35 
24 25 s35 
14 9 6BPh
9 14 6BPh
19 23 2BPh
10 13 6BR
8 14 6BR
JAR3D SCFG/MRF model for IL_16330.1:
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 [25] // Initial node G1194 - C1314 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 [25] // Basepair G1194 - C1314 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | 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 [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | 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 [24] // Basepair A1195 - G1313 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [23] // 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 [4] | Right Index [23] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [23] // 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 [5] | Right Index [23] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [23] // 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 [6] | Right Index [23] // 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 [23] // 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 [7] | Right Index [23] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [7] | Right Index [23] // 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 [23] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.875000000,0.041666667,0.041666667,0.041666667,0.000000000] | Position [1] | Left Index [8] | Right Index [23] // 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 [9] | Right Index [23] // 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 [9] | Right Index [23] // 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 [9] | Right Index [22] // 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 [9] | Right Index [22] // 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 [9] | Right Index [21] // 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 [9] | Right Index [21] // 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 [9] | Right Index [20] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [9] | Right Index [20] // 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 [9] | Right Index [19] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [9] | Right Index [19] // 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 [9] | Right Index [18] // 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 [9] | Right Index [18] // 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 [9] | Right Index [17] // 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 [9] | Right Index [17] // 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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [9] | Right Index [16] // 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 [9] | Right Index [16] // 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 [9] | 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 [2] | Left Index [9] | 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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Left Index [9] | Right Index [14] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.874929957,0.024665076,0.006099772,0.006109041,0.000000000],[0.015780104,0.000174556,0.015006241,0.012399021,0.000000000],[0.007633394,0.014483953,0.000427640,0.000174556,0.000000000],[0.007508515,0.014259062,0.000174556,0.000174556,0.000000000],[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 [9] | Right Index [14] // Basepair A1203 - A1301 tHH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.111901106,0.112896691,0.154434405,0.121632542,0.000000000],[0.130435065,0.118332196,0.001348266,0.117177440,0.000000000],[0.001348266,0.001348266,0.006532064,0.001348266,0.000000000],[0.006420269,0.001348266,0.112148628,0.001348266,0.000000000],[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 [10] | Right Index [13] // Basepair A1204 - G1300 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009250880,0.024435597,0.009809818,0.234417244,0.000000000],[0.020082763,0.009303252,0.192231283,0.010277023,0.000000000],[0.009793103,0.193347778,0.002148094,0.027785070,0.000000000],[0.206751230,0.010349703,0.023586724,0.016430437,0.000000000],[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 A1205 - U1299 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_16330.1:
> IL_16330.1 IL_3U5H_057 G 1194 C 1314
GACACCACAAAA*UGAAAAUGGAUGGCGC
> IL_16330.1 IL_4A1B_058 G 1221 C 1341
GAUACCACAAAA*UGAAAAUGGAUGGCGC