Alignment of IL_28572.2 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
7

2
5
7
I

6
7

3
7
7
I

8
7

4
9
7
I

10
7

5
11
8
I

12
13

6
13
13
I

14
14

7
15
14
I

16
15


17
14
I

18
14

8
19
13
I

20
13

9
21
12
I

22
11

10
23
10
I

24
9

11
25
8
I

26
7

12
27
6
I

28
5

13
29
4
I

30
3

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_28572.2_Instance_1 IL_28572.2_IL_1FJG_021_G515_C536GUGCCAGCGGUAAUAC
IL_28572.2_Sequence_1 IL_28572.2_IL_1FJG_021_G515_C536GUGCCAG*CGGUAAUACtrue100000.00
IL_28572.2_Instance_2 IL_28572.2_IL_2AW7_028_G515_C536GUGCCAGCGGUAAUAC
IL_28572.2_Sequence_2 IL_28572.2_IL_2AW7_028_G515_C536GUGCCAG*CGGUAAUACtrue100000.00
IL_28572.2_Instance_3 IL_28572.2_IL_3U5F_032_G562_C583GUGCCAGCGGUAAUUC
IL_28572.2_Sequence_3 IL_28572.2_IL_3U5F_032_G562_C583GUGCCAG*CGGUAAUUCtrue100000.00
IL_28572.2_Instance_4 IL_28572.2_IL_4BPP_032_G556_C577GUGCCAGCGGUAAUUC
IL_28572.2_Sequence_4 IL_28572.2_IL_4BPP_032_G556_C577GUGCCAG*CGGUAAUUCtrue100000.00

Conserved interactions between motif group positions in IL_28572.2:
1 2 s35 
1 15 cWW 
2 3 s35 
2 5 cSW 
2 12 tWH 
3 11 s35 
3 12 s55 
4 9 s53 
4 10 s35 
5 6 s35 
6 7 s35 
6 9 tHS 
7 8 cWW 
7 9 s55 
7 15 perp 
8 9 s35 
12 15 s35 
3 10 2BPh
4 10 7BPh
3 12 6BPh
15 14 7BPh
12 8 2BR
5 9 7BR
12 14 2BR
7 15 2BR
JAR3D SCFG/MRF model for IL_28572.2:
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 [15] // Initial node G515 - C536 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003876703,0.055283349,0.004488645,0.073569181,0.000000000],[0.006541094,0.022376317,0.079237697,0.005043447,0.000000000],[0.004432143,0.610609112,0.000817354,0.010483940,0.000000000],[0.073144353,0.037059067,0.009043524,0.003994075,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair G515 - C536 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Position [2] | Left Index [2] | Right Index [14] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Position [2] | Left Index [2] | Right Index [13] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [12] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [2] | Right Index [12] | Norm Constant [0.296351259632779] // Cluster node U516:C519 and A533:A533
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.035662906,0.001495870,0.007337569,0.001495870,0.000000000],[0.074292144,0.012419323,0.009929350,0.001495870,0.000000000],[0.007479349,0.001495870,0.017506373,0.006977795,0.000000000],[0.786396396,0.001495870,0.018453857,0.016065588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U516 - A533 tWH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.002332027,0.222432690,0.002869834,0.003093208,0.000000000],[0.004649443,0.223578151,0.002199530,0.003194088,0.000000000],[0.002494052,0.216680046,0.003863335,0.002214343,0.000000000],[0.003415914,0.302790658,0.001922473,0.002270208,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U516 - C519 cSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.002525253,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.002525253,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.992424242,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.002525253,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G517
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.950000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.016666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C518
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [6] | Right Index [11] // Initial node A520 - U531 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Position [2] | Left Index [6] | 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [2] | Left Index [6] | 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.109749162,0.110725601,0.170695282,0.119293454,0.000000000],[0.127926698,0.116056577,0.001322337,0.114924027,0.000000000],[0.001322337,0.001322337,0.006406447,0.001322337,0.000000000],[0.006296802,0.001322337,0.109991924,0.001322337,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A520 - G529 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.004887557,0.009956935,0.005659065,0.092752426,0.000000000],[0.008246692,0.004030138,0.099899013,0.006358532,0.000000000],[0.027939145,0.553701311,0.005152398,0.066088192,0.000000000],[0.092216823,0.006674609,0.011401633,0.005035534,0.000000000],[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 G521 - C528 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_28572.2:
> IL_28572.2 IL_1FJG_021 G  515 C  536
GUGCCAG*CGGUAAUAC
> IL_28572.2 IL_2AW7_028 G  515 C  536
GUGCCAG*CGGUAAUAC
> IL_28572.2 IL_3U5F_032 G  562 C  583
GUGCCAG*CGGUAAUUC
> IL_28572.2 IL_4BPP_032 G  556 C  577
GUGCCAG*CGGUAAUUC