Alignment of IL_83856.1 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
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distance
Alignment
score
deficit
IL_83856.1_Instance_1 IL_83856.1_IL_3U5F_038_G703_C735GCUAACGCGAAC
IL_83856.1_Sequence_1 IL_83856.1_IL_3U5F_038_G703_C735GCUAAC*GCGAAC

Conserved interactions between motif group positions in IL_83856.1:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 cWW 
3 9 s33 
3 10 tWW 
4 5 s35 
4 9 tHS 
4 10 s53 
5 6 s35 
5 8 cWW 
6 7 cWW 
7 8 s35 
8 9 s35 
10 11 s55 
11 12 s35 
10 10 2BPh
10 9 2BR
JAR3D SCFG/MRF model for IL_83856.1:
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 G703 - C735 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G703 - C735 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.012225429,0.015145471,0.014725930,0.034760566,0.000000000],[0.381707213,0.018478793,0.035925510,0.016513221,0.000000000],[0.015080020,0.029754800,0.003718062,0.015583401,0.000000000],[0.042294737,0.014884503,0.334044557,0.015157789,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair C704 - A734 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.036220941,0.005142193,0.001092028,0.011470005,0.000000000],[0.085453464,0.011848042,0.006257264,0.012066093,0.000000000],[0.007644195,0.004596470,0.005402038,0.004976617,0.000000000],[0.774320443,0.014130753,0.012156944,0.007222511,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair U705 - A733 tWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.113009038,0.114014480,0.146062469,0.122836824,0.000000000],[0.131726501,0.119503802,0.001361615,0.118337612,0.000000000],[0.001361615,0.001361615,0.006596738,0.001361615,0.000000000],[0.006483836,0.001361615,0.113259011,0.001361615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A706 - G732 tHS 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.014465575,0.343792072,0.013542226,0.037981708,0.000000000],[0.013601003,0.011560757,0.026720538,0.013366648,0.000000000],[0.013224246,0.032261987,0.003338911,0.299980183,0.000000000],[0.031215838,0.014829276,0.013994275,0.116124756,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A707 - C731 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[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 C708 - G730 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_83856.1:
> IL_83856.1 IL_3U5F_038 G  703 C  735
GCUAAC*GCGAAC