Alignment of IL_86981.1 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
6
I

10
7

5
11
7
I

12
8

6
13
8
I

14
9

7
15
9
I

16
10


17
9
I

18
9

8
19
8
I

20
8

9
21
7
I

22
7

10
23
6
I

24
5

11
25
5
I

26
5

12
27
4
I

28
4

13
29
3
I

30
3

14
31
2
I

32
2

15
33
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_86981.1_Instance_1 IL_86981.1_IL_1S72_013_C290_G362CCGACCGCCAGUACG
IL_86981.1_Sequence_1 IL_86981.1_IL_1S72_013_C290_G362CCGACCG*CCAGUACGtrue100000.00

Conserved interactions between motif group positions in IL_86981.1:
1 2 s35 
1 15 cWW 
2 3 s35 
2 14 bif 
2 15 s55 
3 11 s33 
3 12 s33 
3 13 tSH 
4 5 s35 
4 10 s35 
4 12 tHW 
4 13 s55 
5 6 s35 
5 10 tHH 
6 7 s35 
6 9 bif 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s33 
10 12 s55 
11 12 cSH 
12 13 s35 
13 14 s35 
14 15 s35 
11 4 6BPh
10 5 6BPh
3 12 6BPh
13 3 6BR
JAR3D SCFG/MRF model for IL_86981.1:
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 [15] // Initial node C290 - G362 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | 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 [0.989901010,0.009999000,0.000099990] | 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 [15] // Basepair C290 - G362 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.019872364,0.020657395,0.005619558,0.005619558,0.000000000],[0.290349471,0.571856771,0.005619558,0.005619558,0.000000000],[0.005619558,0.005619558,0.018164488,0.022903933,0.000000000],[0.005619558,0.005619558,0.005619558,0.005619558,0.000000000],[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 [14] // Basepair C291 - C361 bif 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044149057,0.051461378,0.000531940,0.002533030,0.000000000],[0.044541851,0.046686356,0.000531940,0.000531940,0.000000000],[0.382258874,0.003723579,0.018039957,0.309726994,0.000000000],[0.047988462,0.046230763,0.000531940,0.000531940,0.000000000],[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 [13] // Basepair G292 - A360 tSH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [4] | Right Index [12] | Norm Constant [0.460751978306534] // Cluster node A293:A293 and G358:U359
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.026228946,0.054639536,0.005500826,0.559983562,0.000000000],[0.005500826,0.045670107,0.005500826,0.005500826,0.000000000],[0.026982756,0.036513624,0.064376936,0.067861159,0.000000000],[0.005500826,0.005500826,0.025659745,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A293 - U359 tHW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.055679592,0.057359966,0.003128224,0.002588218,0.000000000],[0.053859163,0.062562107,0.000665346,0.063050334,0.000000000],[0.038079735,0.020824015,0.042566873,0.475642955,0.000000000],[0.004791044,0.055793641,0.000665346,0.062743443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G358 - U359 cSH 
InitialNode  | 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 [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.082041499,0.080911814,0.003835387,0.003754037,0.000000000],[0.645166652,0.000907522,0.042266184,0.005341374,0.000000000],[0.025864960,0.074800216,0.002571502,0.000907522,0.000000000],[0.025297269,0.004519016,0.000907522,0.000907522,0.000000000],[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 [10] // Basepair C294 - A357 tHH 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.019872364,0.290349471,0.005619558,0.005619558,0.000000000],[0.020657395,0.571856771,0.005619558,0.005619558,0.000000000],[0.005619558,0.005619558,0.018164488,0.005619558,0.000000000],[0.005619558,0.005619558,0.022903933,0.005619558,0.000000000],[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 [6] | Right Index [9] // Basepair C295 - C356 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 G296 - C355 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_86981.1:
> IL_86981.1 IL_1S72_013 C  290 G  362
CCGACCG*CCAGUACG