Alignment of IL_05221.1 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
4
I

8
4

4
9
4
I

10
4

5
11
5
I

12
6

6
13
6
I

14
7

7
15
7
I

16
8


17
7
I

18
7

8
19
6
I

20
6

9
21
5
I

22
4

10
23
4
I

24
4

11
25
4
I

26
4

12
27
4
I

28
4

13
29
3
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_05221.1_Instance_1 IL_05221.1_IL_3U5H_021_G531_C561GAAUGUAGUAUUAUAGC
IL_05221.1_Sequence_1 IL_05221.1_IL_3U5H_021_G531_C561GAAUGUAG*UAUUAUAGCtrue100000.00

Conserved interactions between motif group positions in IL_05221.1:
1 2 s35 
1 15 cWW 
2 3 s35 
2 10 s33 
2 14 cWW 
3 4 s35 
3 10 tHW 
3 13 bif 
4 5 cSH 
4 9 s33 
4 10 s55 
4 12 tSW 
5 6 s35 
5 11 s55 
5 12 cWH 
5 13 s55 
6 7 s35 
6 9 tHS 
6 12 s53 
7 8 cWW 
8 9 s35 
10 11 cSH 
11 12 s55 
11 13 cWH 
11 14 s35 
13 14 s35 
14 15 s35 
6 9 6BR
2 10 7BR
4 10 6BR
JAR3D SCFG/MRF model for IL_05221.1:
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 [15] // Initial node G531 - C561 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[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 [15] // Basepair G531 - C561 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.315343748,0.019630589,0.493904012,0.022103230,0.000000000],[0.003833930,0.001478680,0.005249063,0.011169182,0.000000000],[0.093002083,0.005315980,0.000968006,0.004364346,0.000000000],[0.004413113,0.011881031,0.004267756,0.003075251,0.000000000],[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 [14] // Basepair A532 - G560 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000001861482761166059500000000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [13] | Norm Constant [0.002186805502869] // Cluster node A533:U536 and U555:A559
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.026228946,0.054639536,0.005500826,0.559983562,0.000000000],[0.005500826,0.045670107,0.005500826,0.005500826,0.000000000],[0.026982756,0.036513624,0.064376936,0.067861159,0.000000000],[0.005500826,0.005500826,0.025659745,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A533 - U555 tHW 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.011713255,0.098795318,0.001115418,0.005321145,0.000000000],[0.103847303,0.005193506,0.005039138,0.004579369,0.000000000],[0.567609822,0.151988445,0.005577088,0.018128417,0.000000000],[0.006756583,0.004694656,0.006215599,0.003424936,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G535 - A557 tSW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U536 - A557 cWH 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.738708947,0.033322493,0.007288080,0.007288080,0.000000000],[0.027777766,0.025772735,0.007288080,0.007288080,0.000000000],[0.007288080,0.007288080,0.058183744,0.043353518,0.000000000],[0.007288080,0.007288080,0.007288080,0.007288080,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A533 - A559 bif 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.066577006,0.068586257,0.003740469,0.003094775,0.000000000],[0.064400289,0.074806542,0.000795565,0.075390323,0.000000000],[0.032523262,0.017785442,0.036355651,0.407683380,0.000000000],[0.005728730,0.066713376,0.000795565,0.075023369,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G535 - U536 cSH 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.111957140,0.109553485,0.005904964,0.004876169,0.000000000],[0.106210408,0.127560275,0.001323815,0.126229679,0.000000000],[0.010119885,0.005598590,0.008485208,0.124838481,0.000000000],[0.007055763,0.106679783,0.001323815,0.142282540,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U555 - U556 cSH 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U556 - A559 cWH 
Insertion    | Location [1] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
Insertion    | Location [6] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 12, position 6 in cluster node
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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.170710115,0.155925473,0.133465681,0.148228098,0.000000000],[0.128906975,0.063872294,0.001608091,0.142674762,0.000000000],[0.001608091,0.001608091,0.013969090,0.001608091,0.000000000],[0.012727400,0.001608091,0.019871564,0.001608091,0.000000000],[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 [6] | Right Index [9] // Basepair A537 - A554 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016663800,0.313360908,0.015725272,0.045114411,0.000000000],[0.014618495,0.011663950,0.038590886,0.015584762,0.000000000],[0.015377247,0.044737484,0.003487844,0.358685405,0.000000000],[0.038297587,0.017266078,0.015312095,0.035513776,0.000000000],[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 G538 - U553 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_05221.1:
> IL_05221.1 IL_3U5H_021 G  531 C  561
GAAUGUAG*UAUUAUAGC