Alignment of IL_00981.1 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
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


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
4

8
19
3
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_00981.1_Instance_1 IL_00981.1,IL_8P9A_299,U1694_A1752UUAACGGAAGA
IL_00981.1_Sequence_1 IL_00981.18P9A_U_1694_A_1752UUAAC*GGAAGAtrue100000.00
IL_00981.1_Instance_2 IL_00981.1,IL_8CRE_076,U1690_A1748UUAACGGAAGA
IL_00981.1_Sequence_2 IL_00981.18CRE_U_1690_A_1748UUAAC*GGAAGAtrue100000.00

Conserved interactions between motif group positions in IL_00981.1:
1 2 s35 
1 10 cWW 
2 8 s35 
2 9 tWH 
3 4 s35 
3 7 s33 
3 8 tHH 
4 5 s35 
4 7 tHS 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s33 
8 9 s55 
9 10 s35 
7 3 6BPh
8 3 6BPh
5 4 7BPh
4 7 6BR
10 9 7BR
JAR3D SCFG/MRF model for IL_00981.1:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.022570428,0.008766396,0.004951663,0.098093613,0.000000000],[0.055072284,0.004912484,0.098423648,0.005518682,0.000000000],[0.024806602,0.097164014,0.001021428,0.011515910,0.000000000],[0.530321662,0.005183742,0.026629096,0.005048348,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U1694 - A1752 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair U1695 - A1750 tWH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.417904513,0.045711150,0.002728011,0.002783222,0.000000000],[0.350402739,0.000568995,0.048507255,0.005406642,0.000000000],[0.019857970,0.047887338,0.001420212,0.000568995,0.000000000],[0.027052588,0.028062379,0.000568995,0.000568995,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A1696 - A1749 tHH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.044022640,0.386803555,0.048778633,0.000000000],[0.046260217,0.046153098,0.003671957,0.045903932,0.000000000],[0.000524565,0.000524565,0.017951032,0.000524565,0.000000000],[0.002472278,0.000524565,0.311661837,0.000524565,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair A1697 - G1748 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003744443,0.006714685,0.004304698,0.078052661,0.000000000],[0.055729281,0.026695245,0.593972767,0.037903304,0.000000000],[0.004353041,0.079734486,0.000820521,0.009213772,0.000000000],[0.079064536,0.005217015,0.010511465,0.003968079,0.000000000],[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 C1698 - G1747 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_00981.1:
> IL_00981.1  8P9A U 1694 A 1752
UUAAC*GGAAGA
> IL_00981.1  8CRE U 1690 A 1748
UUAAC*GGAAGA