Alignment of IL_15840.2 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
6

6
13
7
I

14
8


15
7
I

16
6

7
17
5
I

18
5

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_15840.2_Instance_1 IL_15840.2_IL_2AW7_066_A1430_U1470AAGAAGCCACU
IL_15840.2_Sequence_1 IL_15840.2_IL_2AW7_066_A_1430_U_1470AAGAAG*CCACU
IL_15840.2_Instance_2 IL_15840.2_IL_4A1B_030_U764_G755UAGCAGCCAAG
IL_15840.2_Sequence_2 IL_15840.2_IL_4A1B_030_U764_G755UAGCAG*CCAAG

Conserved interactions between motif group positions in IL_15840.2:
1 2 s35 
1 11 cWW 
2 3 s35 
2 9 s33 
2 10 tSH 
3 8 s33 
3 9 tSH 
4 5 s35 
4 8 tHS 
4 9 s55 
5 6 s35 
5 7 bif 
6 7 cWW 
7 8 s35 
9 10 s35 
10 11 s35 
10 2 6BR
JAR3D SCFG/MRF model for IL_15840.2:
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 A1430 - U1470 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011134496,0.019611426,0.012682293,0.136578475,0.000000000],[0.168530603,0.012682600,0.118742615,0.013871213,0.000000000],[0.012849956,0.116192085,0.002838101,0.021636967,0.000000000],[0.126193227,0.013057190,0.198002729,0.015396023,0.000000000],[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 A1430 - U1470 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.144252810,0.142028198,0.001480190,0.009479171,0.000000000],[0.132612935,0.091907177,0.001480190,0.001480190,0.000000000],[0.132253308,0.001480190,0.010148820,0.066697799,0.000000000],[0.133203331,0.128535313,0.001480190,0.001480190,0.000000000],[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 [10] // Basepair A1431 - C1469 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.111901106,0.130435065,0.001348266,0.006420269,0.000000000],[0.112896691,0.118332196,0.001348266,0.001348266,0.000000000],[0.154434405,0.001348266,0.006532064,0.112148628,0.000000000],[0.121632542,0.117177440,0.001348266,0.001348266,0.000000000],[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 [9] // Basepair G1432 - A1468 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.133737833,0.147730480,0.115492465,0.128805683,0.000000000],[0.111737375,0.195434870,0.001379266,0.124366223,0.000000000],[0.001379266,0.001379266,0.009570662,0.001379266,0.000000000],[0.008780478,0.001379266,0.016068337,0.001379266,0.000000000],[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 [8] // Basepair A1433 - C1467 tHS 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [7] | Norm Constant [0.272972264529784] // Cluster node A1434:G1435 and C1466:C1466
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.019031869,0.608075411,0.004993410,0.004993410,0.000000000],[0.021976200,0.257997875,0.004993410,0.004993410,0.000000000],[0.004993410,0.004993410,0.018938417,0.004993410,0.000000000],[0.004993410,0.004993410,0.024046127,0.004993410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1434 - C1466 bif 
Interaction  | Interacting Bases [2,3] | 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]] // Cluster Interaction G1435 - C1466 cWW 
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 [7] | Right Index [6] // New Initial node after Cluster
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_15840.2:
> IL_15840.2 IL_2AW7_066 A 1430 U 1470
AAGAAG*CCACU
> IL_15840.2 IL_4A1B_030 U  764 G  755
UAGCAG*CCAAG