Alignment of IL_48918.3 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


13
7
I

14
7

6
15
6
I

16
5

7
17
5
I

18
5

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_48918.3_Instance_1 IL_48918.3_IL_4B5R_002_G17_C38GGGAGCGAAGAAC
IL_48918.3_Sequence_1 IL_48918.3_IL_4B5R_002_G17_C38GGGAG*CGAAGAACtrue100000.00
IL_48918.3_Instance_2 IL_48918.3_IL_3UMY_004_G2155_C2136GGGAGCUGUGAAC
IL_48918.3_Sequence_2 IL_48918.3_IL_3UMY_004_G_2155_C_2136GGGAG*CUGUGAACtrue96000.64
IL_48918.3_Instance_3 IL_48918.3_IL_4BW0_001_G3_C23GGGAGCGAAGAAC
IL_48918.3_Sequence_3 IL_48918.3_IL_4BW0_001_G3_C23GGGAG*CGAAGAACtrue100000.00
IL_48918.3_Instance_4 IL_48918.3_IL_4IOA_052_U1426_A1605UGGAGCGUUGAAA
IL_48918.3_Sequence_4 IL_48918.3_IL_4IOA_052_U_1426_A_1605UGGAG*CGUUGAAAtrue96000.65

Conserved interactions between motif group positions in IL_48918.3:
1 2 s35 
1 12 cWW 
2 3 s35 
2 10 s33 
2 11 tSH 
2 12 s55 
3 9 s33 
3 10 tSH 
4 7 tSS 
4 8 s33 
4 9 tHS 
4 10 s55 
5 6 cWW 
5 7 s55 
5 10 perp 
6 7 s35 
8 9 s35 
10 11 s35 
11 12 s35 
2 10 6BPh
11 2 6BR
3 9 6BR
4 9 6BR
5 10 2BR
JAR3D SCFG/MRF model for IL_48918.3:
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 [12] // Initial node G17 - C38 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009734462,0.020214697,0.011090593,0.193143617,0.000000000],[0.018660673,0.008521127,0.200813940,0.012300663,0.000000000],[0.010985401,0.234217224,0.002109217,0.026079210,0.000000000],[0.203918224,0.012767771,0.024324928,0.011118254,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G17 - C38 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.059593935,0.069464361,0.000718031,0.003419172,0.000000000],[0.060124143,0.063018870,0.000718031,0.000718031,0.000000000],[0.342732568,0.003042710,0.014741292,0.253092402,0.000000000],[0.064776498,0.062403894,0.000718031,0.000718031,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G18 - A37 tSH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.067789995,0.079017918,0.000816783,0.003889416,0.000000000],[0.068393123,0.071685967,0.000816783,0.000816783,0.000000000],[0.314619289,0.002761578,0.013379263,0.229707799,0.000000000],[0.073685325,0.070986412,0.000816783,0.000816783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair G19 - A36 tSH 
ClusterNode  | Deletion Probability [0.0000000000031049] | Num Left Bases [1] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.483768278986921] // Cluster node A20:A20 and G32:G35
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.199847682,0.220162527,0.263802060,0.230794523,0.000000000],[0.000898631,0.000898631,0.000898631,0.000898631,0.000000000],[0.004829830,0.005482656,0.008232375,0.059659296,0.000000000],[0.000898631,0.000898631,0.000898631,0.000898631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A20 - G32 tSS 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.106208866,0.107153807,0.197447047,0.115445278,0.000000000],[0.123800031,0.112312816,0.001279681,0.111216801,0.000000000],[0.001279681,0.001279681,0.006199787,0.001279681,0.000000000],[0.006093680,0.001279681,0.106443797,0.001279681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A20 - G35 tHS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A33
Insertion    | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 8, position 3 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006165426,0.012560210,0.007138647,0.117002874,0.000000000],[0.010402818,0.005083832,0.126017962,0.008020992,0.000000000],[0.023812274,0.477595607,0.004391341,0.056326351,0.000000000],[0.116327236,0.008419708,0.014382630,0.006352092,0.000000000],[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 G21 - C31 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_48918.3:
> IL_48918.3 IL_4B5R_002 G   17 C   38
GGGAG*CGAAGAAC
> IL_48918.3 IL_3UMY_004 G 2155 C 2136
GGGAG*CUGUGAAC
> IL_48918.3 IL_4BW0_001 G    3 C   23
GGGAG*CGAAGAAC
> IL_48918.3 IL_4IOA_052 U 1426 A 1605
UGGAG*CGUUGAAA