Alignment of IL_77076.1 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
3

3
7
3
I

8
3

4
9
4
I

10
5


11
4
I

12
3

5
13
3
I

14
3

6
15
3
I

16
3

7
17
3
I

18
3

8
19
3
I

20
3

9
21
3
I

22
3

10
23
3
I

24
3

11
25
3
I

26
3

12
27
3
I

28
3

13
29
3
I

30
3

14
31
3
I

32
3

15
33
3
I

34
3

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_77076.1_Instance_1 IL_77076.1_IL_1MZP_003_G20_C45GGAGCGCCGGUGAAAUAC
IL_77076.1_Sequence_1 IL_77076.1_IL_1MZP_003_G20_C45GGAG*CGCCGGUGAAAUACtrue100000.00
IL_77076.1_Instance_2 IL_77076.1_IL_3UMY_003_G2124_C2174GGAGCGCCGGUGAAAUAC
IL_77076.1_Sequence_2 IL_77076.1_IL_3UMY_003_G_2124_C_2174GGAG*CGCCGGUGAAAUACtrue100000.00

Conserved interactions between motif group positions in IL_77076.1:
1 2 s35 
1 18 cWW 
2 17 tSH 
2 18 s55 
3 6 tSS 
3 17 s55 
4 5 cWW 
4 6 s55 
4 17 tSS 
5 6 s35 
5 17 cSS 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
10 16 tWH 
11 12 s35 
11 15 tWH 
12 15 s55 
13 14 s35 
15 16 s35 
17 18 s35 
8 7 7BPh
12 15 6BPh
2 16 6BPh
18 17 7BPh
17 2 6BR
14 12 7BR
JAR3D SCFG/MRF model for IL_77076.1:
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 [18] // Initial node G20 - C45 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003952716,0.056367336,0.004576658,0.075011714,0.000000000],[0.006669351,0.022815069,0.080791377,0.005142338,0.000000000],[0.004519048,0.602973996,0.000833380,0.010689507,0.000000000],[0.074578555,0.037785716,0.009220848,0.004072390,0.000000000],[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 G20 - C45 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000152587890625000050000000] | Num Left Bases [3] | Num Right Bases [13] | Left Index [2] | Right Index [17] | Norm Constant [0.025236805498983] // Cluster node G21:G23 and C32:A44
Interaction  | Interacting Bases [3,4] | 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]] // Cluster Interaction G23 - C32 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.172411429,0.192167986,0.229920841,0.184388661,0.000000000],[0.002103130,0.002103130,0.002103130,0.002103130,0.000000000],[0.011541768,0.013321536,0.020537534,0.158885204,0.000000000],[0.002103130,0.002103130,0.002103130,0.002103130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A22 - G33 tSS 
Interaction  | Interacting Bases [1,16] | Pair Probability [[0.043716223,0.050956855,0.000526725,0.002508196,0.000000000],[0.044105167,0.046228647,0.000526725,0.000526725,0.000000000],[0.388315159,0.003687073,0.017863095,0.306690455,0.000000000],[0.047517987,0.045777520,0.000526725,0.000526725,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - A44 tSH 
Interaction  | Interacting Bases [3,16] | Pair Probability [[0.027441087,0.006151523,0.007255111,0.006230281,0.000000000],[0.006610097,0.001322019,0.001322019,0.001322019,0.000000000],[0.680617569,0.117598954,0.118861917,0.014691247,0.000000000],[0.006610097,0.001322019,0.001322019,0.001322019,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G23 - A44 tSS 
Interaction  | Interacting Bases [10,14] | Pair Probability [[0.025971800,0.005446896,0.026718220,0.005446896,0.000000000],[0.054103855,0.045222361,0.036155648,0.005446896,0.000000000],[0.005446896,0.005446896,0.063745789,0.025408179,0.000000000],[0.564297448,0.005446896,0.067195854,0.058499471,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A42 tWH 
Interaction  | Interacting Bases [9,15] | Pair Probability [[0.042142294,0.004723046,0.206685502,0.004723046,0.000000000],[0.048779144,0.021003908,0.037384201,0.004723046,0.000000000],[0.004723046,0.004723046,0.032699768,0.491912438,0.000000000],[0.022031629,0.004723046,0.019996218,0.049026621,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G37 - U43 tWH 
Interaction  | Interacting Bases [4,16] | Pair Probability [[0.137353716,0.027973270,0.027144157,0.027605601,0.000000000],[0.265454914,0.028129651,0.003444892,0.025860767,0.000000000],[0.146388091,0.029726665,0.026997642,0.029902458,0.000000000],[0.141951395,0.027674455,0.026559644,0.027832681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C32 - A44 cSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion C34
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.906250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion C35
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G36
Interaction  | Interacting Bases [11,11] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G39
Interaction  | Interacting Bases [12,12] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A40
Interaction  | Interacting Bases [13,13] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A41
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 [5] | Right Index [4] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_77076.1:
> IL_77076.1 IL_1MZP_003 G   20 C   45
GGAG*CGCCGGUGAAAUAC
> IL_77076.1 IL_3UMY_003 G 2124 C 2174
GGAG*CGCCGGUGAAAUAC