Alignment of IL_25181.1 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
5
I

8
10

4
9
10
I

10
11

5
11
11
I

12
12

6
13
12
I

14
13


15
12
I

16
12

7
17
11
I

18
11

8
19
10
I

20
10

9
21
9
I

22
8

10
23
7
I

24
6

11
25
3
I

26
3

12
27
2
I

28
2

13
29
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_25181.1_Instance_1 IL_25181.1_IL_3U5H_080_U1702_G1743UUAUCAUCUUAUG
IL_25181.1_Sequence_1 IL_25181.1_IL_3U5H_080_U_1702_G_1743UUAUCA*UCUUAUGtrue100000.00

Conserved interactions between motif group positions in IL_25181.1:
1 2 s35 
1 13 cWW 
2 10 s33 
2 12 cWW 
2 13 s55 
3 4 s35 
3 9 s33 
3 11 s55 
4 5 s35 
4 9 tHW 
5 6 s35 
5 8 bif 
6 7 cWW 
7 8 s35 
8 9 s35 
9 10 perp 
11 12 s35 
12 13 s35 
12 11 7BPh
JAR3D SCFG/MRF model for IL_25181.1:
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 [13] // Initial node U1702 - G1743 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.013147005,0.014933664,0.015708775,0.039123268,0.000000000],[0.320116843,0.016220977,0.045702007,0.017638328,0.000000000],[0.016064303,0.039422890,0.003563041,0.015642218,0.000000000],[0.046087059,0.015920763,0.366205057,0.014503803,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair U1702 - G1743 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003525330,0.037150057,0.003393454,0.057191747,0.000000000],[0.004354704,0.004432511,0.005124706,0.026189476,0.000000000],[0.003327755,0.005219701,0.001068168,0.076133765,0.000000000],[0.006860857,0.004061194,0.004348111,0.757618463,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [12] // Basepair U1703 - U1742 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [11] // Fixed node on left
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [4] | Right Index [10] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.014555120,0.266044151,0.002936977,0.031543032,0.000000000],[0.002936977,0.018447173,0.002936977,0.002936977,0.000000000],[0.031086478,0.255749148,0.017304204,0.013563416,0.000000000],[0.002936977,0.002936977,0.030486697,0.303598716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair U1705 - U1739 tHW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.019872364,0.290349471,0.005619558,0.005619558,0.000000000],[0.020657395,0.571856771,0.005619558,0.005619558,0.000000000],[0.005619558,0.005619558,0.018164488,0.005619558,0.000000000],[0.005619558,0.005619558,0.022903933,0.005619558,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair C1706 - C1738 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[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 A1707 - U1737 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_25181.1:
> IL_25181.1 IL_3U5H_080 U 1702 G 1743
UUAUCA*UCUUAUG