Alignment of IL_89794.1 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
4
I

10
4

5
11
5
I

12
6


13
5
I

14
4

6
15
4
I

16
4

7
17
4
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_89794.1_Instance_1 IL_89794.1_IL_2QBG_009_G81_C105GUAAGCGUUAUAAC
IL_89794.1_Sequence_1 IL_89794.1_IL_2QBG_009_G81_C105GUAAG*CGUUAUAACtrue100000.00

Conserved interactions between motif group positions in IL_89794.1:
1 2 s35 
1 11 cWW 
2 3 s35 
2 10 tSH 
3 9 tSH 
4 7 tSS 
4 9 s55 
5 6 cWW 
5 7 s55 
5 9 tSS 
6 9 cSS 
7 8 s33 
9 10 s35 
10 11 s35 
JAR3D SCFG/MRF model for IL_89794.1:
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 G81 - C105 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 [11] // Basepair G81 - C105 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.129850760,0.123187903,0.001408720,0.007167075,0.000000000],[0.131556337,0.118915693,0.001408720,0.001408720,0.000000000],[0.127086369,0.001408720,0.008075066,0.065210568,0.000000000],[0.150772980,0.129724929,0.001408720,0.001408720,0.000000000],[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 [10] // Basepair U82 - A104 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214500000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [9] | Norm Constant [0.006232170137623] // Cluster node A83:G85 and C97:A103
Interaction  | Interacting Bases [3,4] | 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]] // Cluster Interaction G85 - C97 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.174118473,0.194070639,0.222296295,0.186214291,0.000000000],[0.002123953,0.002123953,0.002123953,0.002123953,0.000000000],[0.011656043,0.013453433,0.020740876,0.160458324,0.000000000],[0.002123953,0.002123953,0.002123953,0.002123953,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A84 - G98 tSS 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.170710115,0.128906975,0.001608091,0.012727400,0.000000000],[0.155925473,0.063872294,0.001608091,0.001608091,0.000000000],[0.133465681,0.001608091,0.013969090,0.019871564,0.000000000],[0.148228098,0.142674762,0.001608091,0.001608091,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A83 - A103 tSH 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.012966971,0.014534159,0.017141599,0.014720238,0.000000000],[0.003123526,0.003123526,0.003123526,0.003123526,0.000000000],[0.322253558,0.277850187,0.280834180,0.034710902,0.000000000],[0.003123526,0.003123526,0.003123526,0.003123526,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G85 - A103 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.063946723,0.065116510,0.063186491,0.064260646,0.000000000],[0.082864165,0.065480538,0.008019060,0.060199002,0.000000000],[0.068152788,0.069198085,0.062845432,0.069607299,0.000000000],[0.066087230,0.064420927,0.061825857,0.064789247,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C97 - A103 cSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U99
Insertion    | Location [6] | Length Distribution [0.000000000,0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000]// Insertion after nucleotide 8, position 6 in cluster node
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 [6] | Right Index [5] // New Initial node after Cluster
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_89794.1:
> IL_89794.1 IL_2QBG_009 G   81 C  105
GUAAG*CGUUAUAAC