Alignment of IL_87548.1 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
6
I

10
7

5
11
7
I

12
8


13
7
I

14
7

6
15
6
I

16
6

7
17
5
I

18
4

8
19
4
I

20
4

9
21
3
I

22
3

10
23
2
I

24
2

11
25
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_87548.1_Instance_1 IL_87548.1_IL_1FJG_018_G446_C488GGACGCGGUAC
IL_87548.1_Sequence_1 IL_87548.1_IL_1FJG_018_G446_C488GGACG*CGGUACtrue96000.85
IL_87548.1_Instance_2 IL_87548.1_IL_2QBG_067_U1742_G1718UGAAAUAUGUAG
IL_87548.1_Sequence_2 IL_87548.1_IL_2QBG_067_U_1742_G_1718UGAAA*UAUGUAGtrue100000.00

Conserved interactions between motif group positions in IL_87548.1:
1 2 s35 
1 11 cWW 
2 8 s33 
2 9 s33 
2 10 tSH 
2 11 s55 
3 4 s35 
3 7 s35 
3 9 tHW 
3 10 s55 
4 5 s35 
4 7 tWW 
5 6 cWW 
6 7 s33 
7 9 s55 
8 9 cSH 
9 10 s35 
10 11 s35 
8 3 6BPh
2 9 6BPh
10 2 6BR
JAR3D SCFG/MRF model for IL_87548.1:
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 [11] // Initial node G446 - C488 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011606602,0.017778352,0.013679584,0.116107298,0.000000000],[0.167090224,0.012234263,0.126818052,0.015364421,0.000000000],[0.013781309,0.136797428,0.002838808,0.021529953,0.000000000],[0.118996443,0.014843715,0.198100860,0.012432686,0.000000000],[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 [11] // Basepair G446 - C488 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | 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]] | 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 [10] // Basepair G447 - A487 tSH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [9] | Norm Constant [0.464443704046994] // Cluster node A448:A448 and G485:U486
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.025971800,0.054103855,0.005446896,0.564297448,0.000000000],[0.005446896,0.045222361,0.005446896,0.005446896,0.000000000],[0.026718220,0.036155648,0.063745789,0.067195854,0.000000000],[0.005446896,0.005446896,0.025408179,0.058499471,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A448 - U486 tHW 
Interaction  | Interacting Bases [2,3] | 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 G485 - U486 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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.355127970,0.032424063,0.003453240,0.016359048,0.000000000],[0.032464995,0.013376583,0.109435410,0.013192811,0.000000000],[0.003453240,0.010499215,0.326216817,0.018896577,0.000000000],[0.016362695,0.013193067,0.018914099,0.016630170,0.000000000],[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 [7] // Basepair C449 - G484 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009722986,0.022602524,0.010807110,0.213946067,0.000000000],[0.018642384,0.008854915,0.200306720,0.011770232,0.000000000],[0.010724456,0.213953122,0.002148800,0.027678057,0.000000000],[0.199554445,0.012136228,0.023684855,0.013467100,0.000000000],[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 [5] | Right Index [6] // Basepair G450 - C483 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_87548.1:
> IL_87548.1 IL_1FJG_018 G  446 C  488
GGACG*CGGUAC
> IL_87548.1 IL_2QBG_067 U 1742 G 1718
UGAAA*UAUGUAG