Alignment of IL_26868.1 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


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
4

8
19
3
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_26868.1_Instance_1 IL_26868.1_IL_2AW7_022_G446_C488GGAGGCGUUAC
IL_26868.1_Sequence_1 IL_26868.1_IL_2AW7_022_G446_C488GGAGG*CGUUACtrue100000.00

Conserved interactions between motif group positions in IL_26868.1:
1 2 s35 
1 10 cWW 
2 8 s33 
2 9 tSH 
2 10 s55 
3 4 s35 
3 8 tHW 
3 9 s55 
4 5 s35 
4 7 tWW 
4 8 s55 
5 6 cWW 
6 7 s33 
7 8 s55 
8 9 s35 
9 10 s35 
2 8 6BPh
10 9 7BPh
9 2 6BR
JAR3D SCFG/MRF model for IL_26868.1:
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 [10] // Initial node G446 - C488 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003991852,0.056925429,0.004621971,0.075754404,0.000000000],[0.006735384,0.023040960,0.081591292,0.005193253,0.000000000],[0.004563791,0.599043046,0.000841632,0.010795344,0.000000000],[0.075316957,0.038159832,0.009312144,0.004112711,0.000000000],[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 [10] // Basepair G446 - C488 cWW 
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 [2] | Right Index [9] // Basepair G447 - A487 tSH 
BasepairNode | Deletion Probability [0.0000001156129129] | 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]] | 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 [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A448 - U486 tHW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.354264783,0.041072948,0.003750148,0.018657144,0.000000000],[0.038500132,0.015338585,0.012239550,0.015176186,0.000000000],[0.003750148,0.012345288,0.384915834,0.024790969,0.000000000],[0.018551216,0.015162411,0.022954644,0.018530013,0.000000000],[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 [7] // Basepair G449 - G484 tWW 
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 [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_26868.1:
> IL_26868.1 IL_2AW7_022 G  446 C  488
GGAGG*CGUUAC