Alignment of IL_47346.2 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

6
13
7
I

14
8


15
7
I

16
7

7
17
6
I

18
6

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_47346.2_Instance_1 IL_47346.2,IL_8CRE_084,C1914_G1930CGUAACGGAUAAG
IL_47346.2_Sequence_1 IL_47346.28CRE_C_1914_G_1930CGUAAC*GGAUAAGtrue96000.79
IL_47346.2_Instance_2 IL_47346.2,IL_8P9A_307,C1918_G1934CGUAACGGAUAAG
IL_47346.2_Sequence_2 IL_47346.28P9A_C_1918_G_1934CGUAAC*GGAUAAGtrue96000.79
IL_47346.2_Instance_3 IL_47346.2,IL_4V9F_063,C1764_G1780CGUACCGAAGAAG
IL_47346.2_Sequence_3 IL_47346.24V9F_C_1764_G_1780CGUACC*GAAGAAGtrue98000.42
IL_47346.2_Instance_4 IL_47346.2,IL_9DFE_068,C1686_G1702CGUAACGGAGAAG
IL_47346.2_Sequence_4 IL_47346.29DFE_C_1686_G_1702CGUAAC*GGAGAAGtrue100000.00
IL_47346.2_Instance_5 IL_47346.2,IL_7A0S_063,C1703_G1719CGUAACGAAGAAG
IL_47346.2_Sequence_5 IL_47346.27A0S_C_1703_G_1719CGUAAC*GAAGAAGtrue97000.48
IL_47346.2_Instance_6 IL_47346.2,IL_5J7L_308,C1686_G1702CGUAACGGAGAAG
IL_47346.2_Sequence_6 IL_47346.25J7L_C_1686_G_1702CGUAAC*GGAGAAGtrue100000.00
IL_47346.2_Instance_7 IL_47346.2,IL_4WF9_066,C1730_G1746CGUAACGGAGAAG
IL_47346.2_Sequence_7 IL_47346.24WF9_C_1730_G_1746CGUAAC*GGAGAAGtrue100000.00

Conserved interactions between motif group positions in IL_47346.2:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 tSH 
2 12 s55 
3 9 s35 
3 10 tSH 
4 5 s35 
4 8 s33 
4 9 tHH 
4 10 s55 
5 6 s35 
5 8 tHS 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s33 
9 10 s55 
10 11 s35 
11 12 s35 
9 4 6BPh
6 5 7BPh
4 9 6BPh
2 10 6BPh
3 10 6BPh
11 2 6BR
5 8 6BR
JAR3D SCFG/MRF model for IL_47346.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C1914 - G1930 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.041656033,0.044098525,0.000500053,0.002356751,0.000000000],[0.041965507,0.043996411,0.000500053,0.000500053,0.000000000],[0.415457595,0.003500370,0.017112199,0.297098200,0.000000000],[0.046499257,0.043758888,0.000500053,0.000500053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1915 - A1929 tSH 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.044295562,0.040459734,0.000491920,0.002419854,0.000000000],[0.044466678,0.041838855,0.000491920,0.000491920,0.000000000],[0.045742956,0.000491920,0.003040306,0.040838473,0.000000000],[0.409764308,0.318278721,0.003443437,0.003443437,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.055555556,0.055555556,0.611111111,0.277777778,0.000000000] | Left Index [3] | Right Index [10] // Basepair U1916 - A1928 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.726985591,0.075925561,0.004531187,0.004622891,0.000000000],[0.124046326,0.000201430,0.017172088,0.001914009,0.000000000],[0.007029934,0.016952631,0.000502770,0.000201430,0.000000000],[0.009576906,0.009934383,0.000201430,0.000201430,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A1917 - A1926 tHH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.113379207,0.104112383,0.182922785,0.129742854,0.000000000],[0.120606222,0.115065551,0.001434268,0.119892387,0.000000000],[0.001434268,0.001434268,0.007766243,0.001434268,0.000000000],[0.006940992,0.001434268,0.090965772,0.001434268,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1918 - G1925 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003569469,0.006400915,0.004103544,0.074405341,0.000000000],[0.053125109,0.025447804,0.612946003,0.036132122,0.000000000],[0.004149628,0.076008576,0.000782179,0.008783222,0.000000000],[0.075369931,0.004973229,0.010020275,0.003782654,0.000000000],[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 [6] | Right Index [7] // Basepair C1919 - G1924 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_47346.2:
> IL_47346.2  8CRE C 1914 G 1930
CGUAAC*GGAUAAG
> IL_47346.2  8P9A C 1918 G 1934
CGUAAC*GGAUAAG
> IL_47346.2  4V9F C 1764 G 1780
CGUACC*GAAGAAG
> IL_47346.2  9DFE C 1686 G 1702
CGUAAC*GGAGAAG
> IL_47346.2  7A0S C 1703 G 1719
CGUAAC*GAAGAAG
> IL_47346.2  5J7L C 1686 G 1702
CGUAAC*GGAGAAG
> IL_47346.2  4WF9 C 1730 G 1746
CGUAAC*GGAGAAG