Alignment of IL_89028.6 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
5

4
9
5
I

10
5

5
11
5
I

12
5

6
13
5
I

14
5

7
15
5
I

16
5

8
17
5
I

18
5

9
19
6
I

20
7

10
21
7
I

22
8


23
7
I

24
7

11
25
6
I

26
5

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_89028.6_Instance_1 IL_89028.6_IL_3V2F_074_C1934_G1964CGAAAUUCCUUGCCUG
IL_89028.6_Sequence_1 IL_89028.6_IL_3V2F_074_C_1934_G_1964CGAAAUUCCUUG*CCUGtrue100000.00
IL_89028.6_Instance_2 IL_89028.6_IL_4A1B_092_C2272_G2302CCAAAUGCCUCGCGCG
IL_89028.6_Sequence_2 IL_89028.6_IL_4A1B_092_C_2272_G_2302CCAAAUGCCUCG*CGCGtrue93001.52
IL_89028.6_Instance_3 IL_89028.6_IL_2QBG_077_C1934_G1964CGAAAUUCCUUGCCUG
IL_89028.6_Sequence_3 IL_89028.6_IL_2QBG_077_C_1934_G_1964CGAAAUUCCUUG*CCUGtrue100000.00

Conserved interactions between motif group positions in IL_89028.6:
1 2 s35 
1 13 cWW 
2 12 s33 
2 13 s55 
3 6 s33 
3 9 cHW 
3 10 s55 
3 12 tSS 
4 5 s33 
4 6 perp 
6 8 cSH 
7 8 s35 
8 9 s33 
10 11 cWW 
11 12 s35 
11 3 7BPh
12 3 6BPh
2 13 6BPh
7 6 7BR
2 12 6BR
2 13 2BR
JAR3D SCFG/MRF model for IL_89028.6:
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 C1934 - G1964 from junction 
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.009933419,0.017038443,0.011544982,0.190528657,0.000000000],[0.020571967,0.008484264,0.242033011,0.013790371,0.000000000],[0.011692161,0.206400787,0.002129068,0.023556849,0.000000000],[0.191635263,0.013137326,0.027308888,0.010214543,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C1934 - G1964 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.004672897,0.331775701,0.658878505,0.004672897,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [12] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000001936518681344305600000000000000000000000] | Num Left Bases [7] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.407484593358929] // Cluster node A1936:U1943 and C1962:C1962
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.073067940,0.412022438,0.334763565,0.074730107,0.000000000],[0.000848435,0.003498818,0.003288659,0.000848435,0.000000000],[0.004287379,0.017403729,0.030341845,0.036414305,0.000000000],[0.000848435,0.003498818,0.003288659,0.000848435,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1936 - C1962 tSS 
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.059404396,0.065785017,0.016428777,0.012214180,0.000000000],[0.059861207,0.055485992,0.002480374,0.058302387,0.000000000],[0.009643499,0.202599412,0.020015679,0.057773311,0.000000000],[0.185904450,0.136229460,0.002480374,0.055391485,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1940 - C1942 cSH 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.003263974,0.003263974,0.014318437,0.401755682,0.000000000],[0.003263974,0.034912497,0.003263974,0.003263974,0.000000000],[0.016188261,0.016015738,0.013061942,0.261534810,0.000000000],[0.011646306,0.178142997,0.003263974,0.032839487,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1936 - U1943 cHW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1937
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U1939
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.911764706,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C1941
Insertion    | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003914340,0.055820081,0.004532224,0.074283445,0.000000000],[0.006604600,0.022593563,0.080006995,0.005092413,0.000000000],[0.004475173,0.606828618,0.000825289,0.010585725,0.000000000],[0.073854492,0.037418864,0.009131325,0.004032852,0.000000000],[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 [10] | Right Index [11] // Basepair G1945 - C1961 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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_89028.6:
> IL_89028.6 IL_3V2F_074 C 1934 G 1964
CGAAAUUCCUUG*CCUG
> IL_89028.6 IL_4A1B_092 C 2272 G 2302
CCAAAUGCCUCG*CGCG
> IL_89028.6 IL_2QBG_077 C 1934 G 1964
CGAAAUUCCUUG*CCUG