Alignment of IL_97057.3 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

6
13
8
I

14
9


15
8
I

16
8

7
17
7
I

18
7

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_97057.3_Instance_1 IL_97057.3_IL_3V2F_103_G2737_C2767GAUAACGGAAGC
IL_97057.3_Sequence_1 IL_97057.3_IL_3V2F_103_G_2737_C_2767GAUAAC*GGAAGCtrue100000.00
IL_97057.3_Instance_2 IL_97057.3_IL_4IOA_100_G2717_C2747GAUAACGGAAGC
IL_97057.3_Sequence_2 IL_97057.3_IL_4IOA_100_G_2717_C_2747GAUAAC*GGAAGCtrue100000.00
IL_97057.3_Instance_3 IL_97057.3_IL_1S72_094_G2772_C2802GGUAAGCGAAAC
IL_97057.3_Sequence_3 IL_97057.3_IL_1S72_094_G_2772_C_2802GGUAAG*CGAAACtrue98000.33
IL_97057.3_Instance_4 IL_97057.3_IL_4A1B_054_G1193_C1360GAUAAGCGAUAC
IL_97057.3_Sequence_4 IL_97057.3_IL_4A1B_054_G_1193_C_1360GAUAAG*CGAUACtrue92001.19
IL_97057.3_Instance_5 IL_97057.3_IL_2QBG_105_G2737_C2767GAUAAGCGAAAC
IL_97057.3_Sequence_5 IL_97057.3_IL_2QBG_105_G_2737_C_2767GAUAAG*CGAAACtrue99000.10
IL_97057.3_Instance_6 IL_97057.3_IL_1S72_019_A562_U595ACGAAUAGACU
IL_97057.3_Sequence_6 IL_97057.3_IL_1S72_019_A562_U595ACGAAU*AGACUtrue57006.52

Conserved interactions between motif group positions in IL_97057.3:
1 2 s35 
1 11 cWW 
2 3 s35 
2 10 cWW 
3 4 s35 
3 8 s33 
3 9 tWH 
4 5 s35 
4 9 s55 
5 6 s35 
5 8 tHS 
6 7 cWW 
6 8 s55 
7 8 s35 
9 10 s35 
10 11 s35 
8 4 6BPh
5 8 6BR
JAR3D SCFG/MRF model for IL_97057.3:
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 [11] // Initial node G2737 - C2767 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009658942,0.020573664,0.011039066,0.199029485,0.000000000],[0.017014882,0.008233155,0.197928445,0.012283979,0.000000000],[0.010917232,0.250544482,0.002068166,0.026564951,0.000000000],[0.187407283,0.012824330,0.022854039,0.011057898,0.000000000],[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 [11] // Basepair G2737 - C2767 cWW 
BasepairNode | Deletion Probability [0.0000002938397278] | Pair Probability [[0.260225098,0.014136576,0.300019388,0.015073987,0.000000000],[0.012430390,0.032340569,0.017238234,0.029113976,0.000000000],[0.205435835,0.017393028,0.003392668,0.015657552,0.000000000],[0.014952671,0.037776680,0.013879957,0.010933390,0.000000000],[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 [0.170928484,0.821824149,0.006905511,0.000341857] | Right Letter Distribution [0.642857143,0.071428571,0.071428571,0.214285714,0.000000000] | Left Index [2] | Right Index [10] // Basepair A2738 - G2766 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.024501698,0.005138581,0.025205867,0.005138581,0.000000000],[0.051041372,0.042662605,0.034109102,0.005138581,0.000000000],[0.033070509,0.005138581,0.060137537,0.023969980,0.000000000],[0.561027929,0.005138581,0.063392315,0.055188180,0.000000000],[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 [3] | Right Index [9] // Basepair U2739 - A2764 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042066554,0.042440821,0.411397606,0.045724856,0.000000000],[0.049033954,0.044484169,0.003547938,0.044050066,0.000000000],[0.000506848,0.000506848,0.017189016,0.000506848,0.000000000],[0.002413547,0.000506848,0.295117230,0.000506848,0.000000000],[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 [5] | Right Index [8] // Basepair A2741 - G2763 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009584624,0.018740933,0.010993637,0.188045044,0.000000000],[0.018868970,0.008321615,0.219178300,0.012512409,0.000000000],[0.010972503,0.229485735,0.002069217,0.024688148,0.000000000],[0.198595669,0.012606418,0.024755977,0.010580801,0.000000000],[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 C2742 - G2762 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_97057.3:
> IL_97057.3 IL_3V2F_103 G 2737 C 2767
GAUAAC*GGAAGC
> IL_97057.3 IL_4IOA_100 G 2717 C 2747
GAUAAC*GGAAGC
> IL_97057.3 IL_1S72_094 G 2772 C 2802
GGUAAG*CGAAAC
> IL_97057.3 IL_4A1B_054 G 1193 C 1360
GAUAAG*CGAUAC
> IL_97057.3 IL_2QBG_105 G 2737 C 2767
GAUAAG*CGAAAC
> IL_97057.3 IL_1S72_019 A  562 U  595
ACGAAU*AGACU