Alignment of IL_25230.3 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
5

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
8

7
15
8
I

16
9

8
17
9
I

18
10

9
19
10
I

20
11


21
10
I

22
10

10
23
9
I

24
9

11
25
8
I

26
8

12
27
7
I

28
7

13
29
6
I

30
6

14
31
5
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_25230.3_Instance_1 IL_25230.3_IL_1DFU_001_C71_G105CGAUGGUAGCGAGAGUAG
IL_25230.3_Sequence_1 IL_25230.3_IL_1DFU_001_C71_G105CGAUGGUAG*CGAGAGUAGtrue100000.00
IL_25230.3_Instance_2 IL_25230.3_IL_2QBG_005_C71_G105CGAUGGUAGCGAGAGUAG
IL_25230.3_Sequence_2 IL_25230.3_IL_2QBG_005_C71_G105CGAUGGUAG*CGAGAGUAGtrue100000.00
IL_25230.3_Instance_3 IL_25230.3_IL_1FEU_001_C71_G105CGAUGGUAGCGAGAGUAG
IL_25230.3_Sequence_3 IL_25230.3_IL_1FEU_001_C71_G105CGAUGGUAG*CGAGAGUAGtrue100000.00
IL_25230.3_Instance_4 IL_25230.3_IL_3V2F_111_C71_G106CGAUGGUACGGAGAGUAG
IL_25230.3_Sequence_4 IL_25230.3_IL_3V2F_111_C71_G106CGAUGGUAC*GGAGAGUAGtrue100000.09
IL_25230.3_Instance_5 IL_25230.3_IL_4IOA_108_C73_G108CAAUGAUACGAAAAGUCG
IL_25230.3_Sequence_5 IL_25230.3_IL_4IOA_108_C73_G108CAAUGAUAC*GAAAAGUCGtrue88002.61
IL_25230.3_Instance_6 IL_25230.3_IL_364D_003_C97_G79CGAGAGUAGCGAUGGUAG
IL_25230.3_Sequence_6 IL_25230.3_IL_364D_003_C97_G79CGAGAGUAG*CGAUGGUAGtrue79004.41

Conserved interactions between motif group positions in IL_25230.3:
1 2 s35 
1 18 cWW 
2 16 s33 
2 17 tSH 
2 18 s55 
3 4 s35 
3 16 tHW 
3 17 s55 
4 5 s35 
4 15 bif 
5 6 s35 
5 14 wat 
5 15 s55 
6 7 s35 
6 13 bif 
7 8 s35 
7 11 s33 
7 12 tWH 
8 9 s35 
8 11 tHS 
8 12 s55 
9 10 cWW 
9 11 s55 
10 11 s35 
12 13 s35 
13 14 s35 
14 15 s35 
15 16 s35 
16 17 s35 
17 18 s35 
17 2 6BR
8 11 6BR
JAR3D SCFG/MRF model for IL_25230.3:
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 C71 - G105 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009652285,0.016556223,0.011218237,0.185136336,0.000000000],[0.019989741,0.008244143,0.263484907,0.013400077,0.000000000],[0.011361251,0.200559255,0.002068811,0.022890146,0.000000000],[0.186211624,0.012765515,0.026535995,0.009925452,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [18] // Basepair C71 - G105 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.107319836,0.135968602,0.001300561,0.006167642,0.000000000],[0.108304840,0.114225444,0.001300561,0.001300561,0.000000000],[0.176511302,0.001300561,0.006274896,0.108168433,0.000000000],[0.116721758,0.112533879,0.001300561,0.001300561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [17] // Basepair G72 - A104 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.024991732,0.052062200,0.005241353,0.580739054,0.000000000],[0.005241353,0.043515857,0.005241353,0.005241353,0.000000000],[0.025709985,0.034791284,0.061340288,0.064660161,0.000000000],[0.005241353,0.005241353,0.024449379,0.056291944,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [16] // Basepair A73 - U103 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.023615491,0.017319894,0.003739651,0.003739651,0.000000000],[0.300657640,0.014674084,0.003739651,0.003739651,0.000000000],[0.003739651,0.003739651,0.220883287,0.003739651,0.000000000],[0.003739651,0.003739651,0.385453090,0.003739651,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [15] // Basepair U74 - G102 bif 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008042594,0.008042594,0.035974521,0.008042594,0.000000000],[0.008042594,0.008042594,0.008042594,0.008042594,0.000000000],[0.851429169,0.008042594,0.008042594,0.008042594,0.000000000],[0.008042594,0.008042594,0.008042594,0.008042594,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [14] // Basepair G75 - A101 wat 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.062609363,0.236721929,0.003847175,0.003847175,0.000000000],[0.014591112,0.012435492,0.003847175,0.003847175,0.000000000],[0.003847175,0.003847175,0.422453372,0.212716979,0.000000000],[0.003847175,0.003847175,0.003847175,0.003847175,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [13] // Basepair G76 - G100 bif 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.024991732,0.005241353,0.025709985,0.005241353,0.000000000],[0.052062200,0.043515857,0.034791284,0.005241353,0.000000000],[0.005241353,0.005241353,0.061340288,0.024449379,0.000000000],[0.580739054,0.005241353,0.064660161,0.056291944,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [12] // Basepair U77 - A99 tWH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.124703280,0.115292115,0.176480473,0.121074897,0.000000000],[0.125065232,0.105032267,0.001336529,0.116620511,0.000000000],[0.001336529,0.001336529,0.007456337,0.001336529,0.000000000],[0.007169504,0.001336529,0.093086208,0.001336529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [11] // Basepair A78 - G98 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009757676,0.018842539,0.011312047,0.185828079,0.000000000],[0.017698496,0.008140947,0.221507422,0.012975314,0.000000000],[0.011264395,0.242481786,0.002068532,0.025317133,0.000000000],[0.185469795,0.013186749,0.024102342,0.010046747,0.000000000],[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 G79 - C97 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_25230.3:
> IL_25230.3 IL_1DFU_001 C   71 G  105
CGAUGGUAG*CGAGAGUAG
> IL_25230.3 IL_2QBG_005 C   71 G  105
CGAUGGUAG*CGAGAGUAG
> IL_25230.3 IL_1FEU_001 C   71 G  105
CGAUGGUAG*CGAGAGUAG
> IL_25230.3 IL_3V2F_111 C   71 G  106
CGAUGGUAC*GGAGAGUAG
> IL_25230.3 IL_4IOA_108 C   73 G  108
CAAUGAUAC*GAAAAGUCG
> IL_25230.3 IL_364D_003 C   97 G   79
CGAGAGUAG*CGAUGGUAG