Alignment of IL_09882.1 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
4
I

8
5

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
8


15
7
I

16
7

7
17
6
I

18
6

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_09882.1_Instance_1 IL_09882.1_IL_1KD5_001_U3_G8UCACAGUCACAG
IL_09882.1_Sequence_1 IL_09882.1_IL_1KD5_001_U3_G8UCACAG*UCACAGtrue100000.02
IL_09882.1_Instance_2 IL_09882.1_IL_283D_001_C4_G9CGAAAGCGAAAG
IL_09882.1_Sequence_2 IL_09882.1_IL_283D_001_C4_G9CGAAAG*CGAAAGtrue100000.00

Conserved interactions between motif group positions in IL_09882.1:
1 2 s35 
1 12 cWW 
2 11 tSH 
2 12 s55 
3 4 s35 
3 10 tHW 
3 11 s55 
4 5 s35 
4 9 tWH 
4 10 s55 
5 6 s35 
5 8 tHS 
5 9 s55 
6 7 cWW 
6 8 s55 
7 8 s35 
9 10 s35 
10 11 s35 
11 12 s35 
11 2 6BR
5 8 6BR
JAR3D SCFG/MRF model for IL_09882.1:
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 [12] // Initial node U3 - G8 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011524459,0.015996371,0.013606468,0.115568146,0.000000000],[0.168876048,0.012314695,0.139927955,0.015695487,0.000000000],[0.013856800,0.123730358,0.002839025,0.019638331,0.000000000],[0.119574633,0.014515400,0.199997678,0.012338148,0.000000000],[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 [12] // Basepair U3 - G8 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.129506361,0.126673089,0.001432729,0.008039397,0.000000000],[0.142111874,0.112243512,0.001432729,0.001432729,0.000000000],[0.140738059,0.001432729,0.008529896,0.064911900,0.000000000],[0.131659396,0.126990143,0.001432729,0.001432729,0.000000000],[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 [11] // Basepair C4 - A7 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.218999763,0.151281779,0.003250143,0.021991785,0.000000000],[0.003250143,0.013270599,0.003250143,0.003250143,0.000000000],[0.241326746,0.127991387,0.033272604,0.017815985,0.000000000],[0.003250143,0.003250143,0.030767019,0.123781475,0.000000000],[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 [10] // Basepair A5 - C6 tHW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.218999763,0.003250143,0.241326746,0.003250143,0.000000000],[0.151281779,0.013270599,0.127991387,0.003250143,0.000000000],[0.003250143,0.003250143,0.033272604,0.030767019,0.000000000],[0.021991785,0.003250143,0.017815985,0.123781475,0.000000000],[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 [9] // Basepair C6 - A5 tWH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.129506361,0.142111874,0.140738059,0.131659396,0.000000000],[0.126673089,0.112243512,0.001432729,0.126990143,0.000000000],[0.001432729,0.001432729,0.008529896,0.001432729,0.000000000],[0.008039397,0.001432729,0.064911900,0.001432729,0.000000000],[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 [5] | Right Index [8] // Basepair A7 - C4 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013347761,0.165529096,0.013687752,0.119073501,0.000000000],[0.015838591,0.009978088,0.123297350,0.014347705,0.000000000],[0.013441150,0.139428673,0.002801578,0.196271923,0.000000000],[0.115139890,0.015509778,0.019472481,0.022834682,0.000000000],[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 [6] | Right Index [7] // Basepair G8 - U3 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_09882.1:
> IL_09882.1 IL_1KD5_001 U    3 G    8
UCACAG*UCACAG
> IL_09882.1 IL_283D_001 C    4 G    9
CGAAAG*CGAAAG