Alignment of IL_97833.1 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
4

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
8

7
15
8
I

16
9


17
8
I

18
8

8
19
7
I

20
7

9
21
6
I

22
6

10
23
5
I

24
4

11
25
4
I

26
4

12
27
3
I

28
3

13
29
2
I

30
2

14
31
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_97833.1_Instance_1 IL_97833.1_IL_1LNG_003_G200_C221GCCAGGCGAGCAAC
IL_97833.1_Sequence_1 IL_97833.1_IL_1LNG_003_G200_C221GCCAGGC*GAGCAACtrue100000.00
IL_97833.1_Instance_2 IL_97833.1_IL_3KTW_004_G201_C222GCCAGGCGAGCAAC
IL_97833.1_Sequence_2 IL_97833.1_IL_3KTW_004_G201_C222GCCAGGC*GAGCAACtrue100000.00

Conserved interactions between motif group positions in IL_97833.1:
1 2 s35 
1 14 cWW 
2 3 s35 
2 13 cSW 
3 10 s33 
3 11 tWH 
3 12 tSH 
4 5 s35 
4 11 tHW 
4 12 s55 
5 6 s35 
5 10 tHS 
6 7 s35 
6 9 cWW 
6 10 s55 
7 8 cWW 
8 9 s35 
9 10 s35 
10 11 s35 
11 12 s35 
12 13 s35 
13 14 s35 
10 4 6BPh
3 11 6BPh
12 3 6BR
JAR3D SCFG/MRF model for IL_97833.1:
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 [14] // Initial node G200 - C221 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 [14] // Basepair G200 - C221 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.180898075,0.022979953,0.009978689,0.007794541,0.000000000],[0.223106457,0.018378246,0.010047856,0.008559157,0.000000000],[0.175423867,0.020184915,0.094841633,0.006698679,0.000000000],[0.184471354,0.020276628,0.009230277,0.007129673,0.000000000],[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 [13] // Basepair C201 - A220 cSW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [12] | Norm Constant [0.332826416872369] // Cluster node C202:A203 and C218:A219
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.004434773,0.001207200,0.004843947,0.001207200,0.000000000],[0.039987114,0.864647803,0.038094142,0.008450400,0.000000000],[0.001207200,0.001207200,0.005505466,0.005368552,0.000000000],[0.010022668,0.001207200,0.005026705,0.007582431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C202 - C218 tWH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.019854918,0.271099652,0.002514918,0.024980606,0.000000000],[0.002514918,0.011900540,0.002514918,0.002514918,0.000000000],[0.140902150,0.233169698,0.017178551,0.012038356,0.000000000],[0.002514918,0.002514918,0.025973821,0.227812200,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A203 - C218 tHW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.056651997,0.047332496,0.000584264,0.003719453,0.000000000],[0.428592377,0.286158103,0.004089845,0.004089845,0.000000000],[0.048923171,0.000584264,0.004054179,0.006806626,0.000000000],[0.054562714,0.052682138,0.000584264,0.000584264,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C202 - A219 tSH 
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 [5] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009247054,0.007386523,0.036100978,0.006101933,0.000000000],[0.005030892,0.004674688,0.007451505,0.005316705,0.000000000],[0.001064501,0.001064501,0.764758390,0.001064501,0.000000000],[0.099309926,0.001064501,0.049298902,0.001064501,0.000000000],[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 [10] // Basepair G204 - G217 tHS 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.045558309,0.014099396,0.342018043,0.016229361,0.000000000],[0.014438420,0.005788124,0.019549681,0.043692861,0.000000000],[0.375595066,0.019303593,0.003559872,0.015694806,0.000000000],[0.016257062,0.041075014,0.016050017,0.011090375,0.000000000],[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 [6] | Right Index [9] // Basepair G205 - A216 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 [7] | Right Index [8] // Basepair C206 - G215 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_97833.1:
> IL_97833.1 IL_1LNG_003 G  200 C  221
GCCAGGC*GAGCAAC
> IL_97833.1 IL_3KTW_004 G  201 C  222
GCCAGGC*GAGCAAC