Alignment of IL_94744.1 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
8

4
9
8
I

10
9

5
11
9
I

12
10

6
13
10
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
11
I

26
10

12
27
9
I

28
9

13
29
8
I

30
8

14
31
7
I

32
6

15
33
3
I

34
3

16
35
2
I

36
2

17
37
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_94744.1_Instance_1 IL_94744.1_IL_3D0U_003_G19_C67GAUGAGUAGUGAAAGGC
IL_94744.1_Sequence_1 IL_94744.1_IL_3D0U_003_G19_C67GAUGAGUAG*UGAAAGGCtrue100000.00
IL_94744.1_Instance_2 IL_94744.1_IL_3DIR_003_G22_C70GAUGAGUAGUGAAAGGC
IL_94744.1_Sequence_2 IL_94744.1_IL_3DIR_003_G22_C70GAUGAGUAG*UGAAAGGCtrue100000.00

Conserved interactions between motif group positions in IL_94744.1:
1 2 s35 
1 17 cWW 
2 3 s35 
2 16 cWW 
3 4 s35 
4 5 s33 
4 13 s33 
4 14 tSH 
5 6 s55 
5 7 s55 
5 12 s53 
5 13 tHH 
6 7 cSH 
6 11 s33 
7 8 s35 
7 11 s33 
7 12 tWH 
8 9 s35 
8 11 tHS 
8 12 s55 
9 10 cWW 
10 11 s35 
12 13 s35 
13 14 s35 
14 15 s35 
15 16 s35 
16 17 s35 
11 7 6BPh
6 12 6BPh
5 13 6BPh
14 4 6BR
11 6 6BR
8 11 6BR
JAR3D SCFG/MRF model for IL_94744.1:
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 [17] // Initial node G19 - C67 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 [17] // Basepair G19 - C67 cWW 
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 [2] | Right Index [16] // Basepair A20 - G66 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [3] | Right Index [15] // 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 [15] // 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 [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 [[0.111901106,0.130435065,0.001348266,0.006420269,0.000000000],[0.112896691,0.118332196,0.001348266,0.001348266,0.000000000],[0.154434405,0.001348266,0.006532064,0.112148628,0.000000000],[0.121632542,0.117177440,0.001348266,0.001348266,0.000000000],[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 [4] | Right Index [14] // Basepair G22 - A64 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.562260899,0.109540081,0.027089699,0.027130866,0.000000000],[0.010011575,0.000775219,0.066644223,0.055065299,0.000000000],[0.004842953,0.064324690,0.001899191,0.000775219,0.000000000],[0.004763724,0.063325924,0.000775219,0.000775219,0.000000000],[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 [13] // Basepair A23 - A63 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [6] | Right Index [12] | Norm Constant [0.464443704046994] // Cluster node G24:U25 and A62:A62
Interaction  | Interacting Bases [2,3] | 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 U25 - A62 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.055133713,0.056797613,0.003097555,0.002562843,0.000000000],[0.053331132,0.061948753,0.000658823,0.062432193,0.000000000],[0.037706404,0.020619858,0.042149551,0.480783711,0.000000000],[0.004744073,0.055246645,0.000658823,0.062128311,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G24 - U25 cSH 
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 [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] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043716223,0.044105167,0.388315159,0.047517987,0.000000000],[0.050956855,0.046228647,0.003687073,0.045777520,0.000000000],[0.000526725,0.000526725,0.017863095,0.000526725,0.000000000],[0.002508196,0.000526725,0.306690455,0.000526725,0.000000000],[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 - G61 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[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 G27 - U60 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_94744.1:
> IL_94744.1 IL_3D0U_003 G   19 C   67
GAUGAGUAG*UGAAAGGC
> IL_94744.1 IL_3DIR_003 G   22 C   70
GAUGAGUAG*UGAAAGGC