Alignment of IL_37197.1 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
9
I

12
10

6
13
10
I

14
11

7
15
11
I

16
12


17
11
I

18
11

8
19
10
I

20
10

9
21
9
I

22
9

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_37197.1_Instance_1 IL_37197.1_IL_3U5H_082_A1883_U2349AAUAAUGCUAU
IL_37197.1_Sequence_1 IL_37197.1_IL_3U5H_082_A_1883_U_2349AAUAAUG*CUAUtrue100000.00
IL_37197.1_Instance_2 IL_37197.1_IL_4A1B_078_A1907_U2344AACAAUGCUAU
IL_37197.1_Sequence_2 IL_37197.1_IL_4A1B_078_A_1907_U_2344AACAAUG*CUAUtrue100000.00

Conserved interactions between motif group positions in IL_37197.1:
1 2 s35 
1 11 cWW 
2 3 s35 
4 5 s35 
5 6 s35 
5 10 tHS 
6 7 s35 
6 9 cWW 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s35 
10 11 s35 
11 10 7BPh
5 10 6BR
JAR3D SCFG/MRF model for IL_37197.1:
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 A1883 - U2349 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003493366,0.009227499,0.003704435,0.587430059,0.000000000],[0.007583759,0.003513143,0.072591391,0.027166046,0.000000000],[0.003698123,0.073013008,0.000811175,0.073446414,0.000000000],[0.078074490,0.003908310,0.008906943,0.043431838,0.000000000],[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 [1] | Right Index [11] // Basepair A1883 - U2349 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.178840408,0.154396792,0.132157194,0.146774881,0.000000000],[0.127643181,0.063246095,0.001592326,0.141275990,0.000000000],[0.001592326,0.001592326,0.013832138,0.001592326,0.000000000],[0.012602622,0.001592326,0.019676744,0.001592326,0.000000000],[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 [5] | Right Index [10] // Basepair A1887 - A2348 tHS 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.016266706,0.171419124,0.015658197,0.037699458,0.000000000],[0.020093633,0.020452651,0.023646600,0.017263489,0.000000000],[0.015355045,0.024084933,0.004928778,0.050185592,0.000000000],[0.031657613,0.018739307,0.020063209,0.512485663,0.000000000],[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 [6] | Right Index [9] // Basepair U1888 - U2347 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[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 [7] | Right Index [8] // Basepair G1889 - C2346 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_37197.1:
> IL_37197.1 IL_3U5H_082 A 1883 U 2349
AAUAAUG*CUAU
> IL_37197.1 IL_4A1B_078 A 1907 U 2344
AACAAUG*CUAU