Alignment of IL_27243.1 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
2

2
5
2
I

6
2

3
7
3
I

8
4

4
9
4
I

10
5


11
4
I

12
4

5
13
3
I

14
2

6
15
2
I

16
2

7
17
2
I

18
2

8
19
2
I

20
2

9
21
2
I

22
2

10
23
2
I

24
2

11
25
2
I

26
2

12
27
2
I

28
2

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_27243.1_Instance_1 IL_27243.1_IL_3D2V_002_G10_C36GGUGCUGAGAAAGUC
IL_27243.1_Sequence_1 IL_27243.1_IL_3D2V_002_G10_C36GGUG*CUGAGAAAGUCtrue100000.00

Conserved interactions between motif group positions in IL_27243.1:
1 2 s35 
1 14 cWW 
2 3 s35 
2 9 tSS 
2 13 cWH 
3 11 s33 
3 12 cWH 
4 5 cWW 
4 10 s53 
5 6 s35 
6 7 s35 
6 10 tWH 
7 9 s33 
7 10 s55 
8 9 s35 
8 14 cSS 
12 13 s53 
13 14 s55 
11 4 2BPh
7 10 6BPh
JAR3D SCFG/MRF model for IL_27243.1:
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 G10 - C36 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000000001191720873277651700000000000000] | Num Left Bases [3] | Num Right Bases [9] | Left Index [1] | Right Index [14] | Norm Constant [0.124973342635811] // Cluster node G10:U12 and U27:C36
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.011418641,0.014331648,0.024329846,0.014025501,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.224007246,0.230872701,0.259048862,0.202033724,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - G30 tSS 
Interaction  | Interacting Bases [3,10] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U12 - A33 cWH 
Interaction  | Interacting Bases [2,11] | Pair Probability [[0.004796933,0.004796933,0.048610550,0.028102840,0.000000000],[0.004796933,0.045138252,0.223369287,0.025351263,0.000000000],[0.037055570,0.004796933,0.489594339,0.004796933,0.000000000],[0.019196620,0.004796933,0.014757791,0.040041888,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - G34 cWH 
Interaction  | Interacting Bases [1,12] | 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 G10 - C36 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.026228946,0.005500826,0.026982756,0.005500826,0.000000000],[0.054639536,0.045670107,0.036513624,0.005500826,0.000000000],[0.005500826,0.005500826,0.064376936,0.025659745,0.000000000],[0.559983562,0.005500826,0.067861159,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U27 - A31 tWH 
Interaction  | Interacting Bases [6,12] | Pair Probability [[0.069980681,0.084135701,0.070448286,0.071021101,0.000000000],[0.066251302,0.064644197,0.006795540,0.066652281,0.000000000],[0.067719711,0.066936321,0.060177817,0.067928475,0.000000000],[0.067869819,0.037376987,0.062185642,0.069876138,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A29 - C36 cSS 
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G28
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A32
Insertion    | Location [11] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 13, position 11 in cluster node
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 [4] | Right Index [5] // New Initial node after Cluster
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 [4] | Right Index [5] // Basepair G13 - C26 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_27243.1:
> IL_27243.1 IL_3D2V_002 G   10 C   36
GGUG*CUGAGAAAGUC