Alignment of IL_72158.3 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
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_72158.3_Instance_1 IL_72158.3_IL_3U5H_086_C1918_G1934CGUAACGGAUAAG
IL_72158.3_Sequence_1 IL_72158.3_IL_3U5H_086_C_1918_G_1934CGUAAC*GGAUAAGtrue97000.59
IL_72158.3_Instance_2 IL_72158.3_IL_4IOA_063_C1703_G1719CGUAACGAAGAAG
IL_72158.3_Sequence_2 IL_72158.3_IL_4IOA_063_C_1703_G_1719CGUAAC*GAAGAAGtrue98000.29
IL_72158.3_Instance_3 IL_72158.3_IL_2QBG_066_C1686_G1702CGUAACGGAGAAG
IL_72158.3_Sequence_3 IL_72158.3_IL_2QBG_066_C_1686_G_1702CGUAAC*GGAGAAGtrue100000.00
IL_72158.3_Instance_4 IL_72158.3_IL_1S72_063_C1764_G1780CGUACCGAAGAAG
IL_72158.3_Sequence_4 IL_72158.3_IL_1S72_063_C_1764_G_1780CGUACC*GAAGAAGtrue99000.21
IL_72158.3_Instance_5 IL_72158.3_IL_4A1B_082_C1942_G1958CGUAACGGAUAAG
IL_72158.3_Sequence_5 IL_72158.3_IL_4A1B_082_C_1942_G_1958CGUAAC*GGAUAAGtrue97000.59
IL_72158.3_Instance_6 IL_72158.3_IL_3V2F_065_C1686_G1702CGUAACGGAGAAG
IL_72158.3_Sequence_6 IL_72158.3_IL_3V2F_065_C_1686_G_1702CGUAAC*GGAGAAGtrue100000.00

Conserved interactions between motif group positions in IL_72158.3:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 tSH 
2 12 s55 
3 9 s35 
3 10 tSH 
3 11 s55 
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
4 9 6BPh
2 10 6BPh
3 10 6BPh
11 2 6BR
5 8 6BR
JAR3D SCFG/MRF model for IL_72158.3:
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 C1918 - G1934 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009652285,0.016556223,0.011218237,0.185136336,0.000000000],[0.019989741,0.008244143,0.263484907,0.013400077,0.000000000],[0.011361251,0.200559255,0.002068811,0.022890146,0.000000000],[0.186211624,0.012765515,0.026535995,0.009925452,0.000000000],[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 C1918 - G1934 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042066554,0.049033954,0.000506848,0.002413547,0.000000000],[0.042440821,0.044484169,0.000506848,0.000506848,0.000000000],[0.411397606,0.003547938,0.017189016,0.295117230,0.000000000],[0.045724856,0.044050066,0.000506848,0.000506848,0.000000000],[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 G1919 - A1933 tSH 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.046567858,0.044178385,0.000505204,0.002570300,0.000000000],[0.047179522,0.042646259,0.000505204,0.000505204,0.000000000],[0.045576476,0.000505204,0.002895928,0.023386205,0.000000000],[0.410246278,0.325659125,0.003536425,0.003536425,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.062500000,0.562500000,0.312500000,0.000000000] | Left Index [3] | Right Index [10] // Basepair U1920 - A1932 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.882009394,0.023268940,0.005754502,0.005763247,0.000000000],[0.014886891,0.000164675,0.014156831,0.011697190,0.000000000],[0.007201315,0.013664107,0.000403434,0.000164675,0.000000000],[0.007083505,0.013451945,0.000164675,0.000164675,0.000000000],[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 A1921 - A1930 tHH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.124344693,0.114960517,0.166649233,0.120754020,0.000000000],[0.135520847,0.105390881,0.001339703,0.116398741,0.000000000],[0.001339703,0.001339703,0.007445662,0.001339703,0.000000000],[0.007159152,0.001339703,0.093338037,0.001339703,0.000000000],[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 A1922 - G1929 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009652285,0.016556223,0.011218237,0.185136336,0.000000000],[0.019989741,0.008244143,0.263484907,0.013400077,0.000000000],[0.011361251,0.200559255,0.002068811,0.022890146,0.000000000],[0.186211624,0.012765515,0.026535995,0.009925452,0.000000000],[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 C1923 - G1928 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_72158.3:
> IL_72158.3 IL_3U5H_086 C 1918 G 1934
CGUAAC*GGAUAAG
> IL_72158.3 IL_4IOA_063 C 1703 G 1719
CGUAAC*GAAGAAG
> IL_72158.3 IL_2QBG_066 C 1686 G 1702
CGUAAC*GGAGAAG
> IL_72158.3 IL_1S72_063 C 1764 G 1780
CGUACC*GAAGAAG
> IL_72158.3 IL_4A1B_082 C 1942 G 1958
CGUAAC*GGAUAAG
> IL_72158.3 IL_3V2F_065 C 1686 G 1702
CGUAAC*GGAGAAG