Alignment of IL_58126.1 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
5
I

8
6

4
9
6
I

10
7

5
11
7
I

12
8

6
13
8
I

14
9

7
15
9
I

16
10

8
17
10
I

18
11


19
10
I

20
10

9
21
9
I

22
9

10
23
8
I

24
8

11
25
7
I

26
7

12
27
6
I

28
6

13
29
5
I

30
5

14
31
2
I

32
2

15
33
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_58126.1_Instance_1 IL_58126.1,IL_6VMY_004,C326_G348CACGAAUUACAGAUG
IL_58126.1_Sequence_1 IL_58126.16VMY_C326_G348CACGAAUU*ACAGAUGtrue91001.82
IL_58126.1_Instance_2 IL_58126.1,IL_8P9A_247,G517_C573GGAUAAAUCGGAAUAC
IL_58126.1_Sequence_2 IL_58126.18P9A_G517_C573GGAUAAAUC*GGAAUACtrue100000.00

Conserved interactions between motif group positions in IL_58126.1:
1 2 s33 
1 15 cWW 
2 3 s55 
2 15 s35 
3 14 cWW 
4 5 s35 
4 13 tHW 
4 14 s55 
5 6 s35 
5 12 tHW 
6 7 s35 
6 11 tHW 
6 12 s55 
7 8 s35 
7 10 bif 
7 12 s55 
8 9 cWW 
9 10 s35 
10 11 s35 
11 12 s35 
12 13 s35 
14 15 s35 
2 2 2BPh
JAR3D SCFG/MRF model for IL_58126.1:
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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 [15] // Basepair C326 - G348 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.468750000,0.031250000,0.468750000,0.031250000,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 6VMY|1|A|A|327
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 [14] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.113901243,0.013673404,0.039993729,0.017216886,0.000000000],[0.015004034,0.011757907,0.022387621,0.349053083,0.000000000],[0.042256649,0.021570042,0.003392492,0.015062512,0.000000000],[0.018329330,0.287884191,0.016452883,0.012063996,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | 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 [14] // Basepair C328 - U347 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.017068734,0.037986112,0.003777338,0.387537728,0.000000000],[0.003777338,0.304381264,0.009054529,0.003777338,0.000000000],[0.116659155,0.003777338,0.028726337,0.021915662,0.000000000],[0.003777338,0.003777338,0.016800299,0.037206152,0.000000000],[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 [13] // Basepair G329 - A346 tHW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.338510258,0.028135304,0.102217545,0.014853320,0.000000000],[0.003287063,0.013949136,0.008142503,0.003287063,0.000000000],[0.289978051,0.003287063,0.120823975,0.015754893,0.000000000],[0.003287063,0.003287063,0.035183695,0.016016004,0.000000000],[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 [12] // Basepair A330 - G345 tHW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.437440739,0.028135304,0.003287063,0.014853320,0.000000000],[0.003287063,0.013949136,0.008142503,0.003287063,0.000000000],[0.289978051,0.003287063,0.120823975,0.015754893,0.000000000],[0.003287063,0.003287063,0.035183695,0.016016004,0.000000000],[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 [11] // Basepair A331 - A344 tHW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.042606139,0.021817912,0.003408043,0.003408043,0.000000000],[0.278708956,0.013066348,0.003408043,0.003408043,0.000000000],[0.003408043,0.003408043,0.160181528,0.003408043,0.000000000],[0.003408043,0.102338524,0.350608208,0.003408043,0.000000000],[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 [7] | Right Index [10] // Basepair U332 - C343 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009285457,0.017323068,0.010436779,0.197555258,0.000000000],[0.021160175,0.009772202,0.212782490,0.012417770,0.000000000],[0.010508004,0.198766713,0.002067002,0.023256875,0.000000000],[0.212699647,0.011830790,0.040032900,0.010104868,0.000000000],[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 [8] | Right Index [9] // Basepair U333 - A342 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_58126.1:
> IL_58126.1  6VMY C  326 G  348
CACGAAUU*ACAGAUG
> IL_58126.1  8P9A G  517 C  573
GGAUAAAUC*GGAAUAC