Alignment of IL_58103.11 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
3
I

10
4

5
11
5
I

12
6


13
5
I

14
4

6
15
4
I

16
4

7
17
4
I

18
4

8
19
4
I

20
4

9
21
3
I

22
2

10
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_58103.11_Instance_1 IL_58103.11,IL_4V9F_104,U33_A47UACCCGAACA
IL_58103.11_Sequence_1 IL_58103.114V9F_U33_A47UACCC*GAACAtrue92001.25
IL_58103.11_Instance_2 IL_58103.11,IL_5NS3_002,A34_U48ACCCCGAACU
IL_58103.11_Sequence_2 IL_58103.115NS3_A34_U48ACCCC*GAACUtrue100000.00
IL_58103.11_Instance_3 IL_58103.11,IL_9DFE_113,U34_A48UUCCCGAACA
IL_58103.11_Sequence_3 IL_58103.119DFE_U34_A48UUCCC*GAACAtrue97000.41
IL_58103.11_Instance_4 IL_58103.11,IL_8OI5_138,U32_A45UCCCCGAUCA
IL_58103.11_Sequence_4 IL_58103.118OI5_U32_A45UCCCC*GAUCAtrue93001.17
IL_58103.11_Instance_5 IL_58103.11,IL_8P9A_368,U32_A45UUCCCGAUCA
IL_58103.11_Sequence_5 IL_58103.118P9A_U32_A45UUCCC*GAUCAtrue90001.62
IL_58103.11_Instance_6 IL_58103.11,IL_4WF9_115,U32_A46UUCCCGAACA
IL_58103.11_Sequence_6 IL_58103.114WF9_U32_A46UUCCC*GAACAtrue97000.41
IL_58103.11_Instance_7 IL_58103.11,IL_5J7L_358,A34_U48ACCCCGAACU
IL_58103.11_Sequence_7 IL_58103.115J7L_A34_U48ACCCC*GAACUtrue100000.00
IL_58103.11_Instance_8 IL_58103.11,IL_7A0S_113,A36_U50ACCCCGAACU
IL_58103.11_Sequence_8 IL_58103.117A0S_A36_U50ACCCC*GAACUtrue100000.00
IL_58103.11_Instance_9 IL_58103.11,IL_1MJI_004,A34_U48ACCCCGAACU
IL_58103.11_Sequence_9 IL_58103.111MJI_A34_U48ACCCC*GAACUtrue100000.00

Conserved interactions between motif group positions in IL_58103.11:
1 6 s33 
1 10 cWW 
2 3 s35 
4 5 s35 
4 10 cWS 
5 6 cWW 
6 9 tSW 
6 10 s35 
7 8 s35 
8 9 s35 
9 10 s35 
5 4 7BPh
8 6 7BR
JAR3D SCFG/MRF model for IL_58103.11:
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 [10] // Initial node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [10] | Norm Constant [0.256806238322926] // Cluster node 4V9F|1|9|U|33:4V9F|1|9|C|36 and 4V9F|1|9|A|47:4V9F|1|9|A|47
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.008557538,0.018275361,0.009275439,0.223652173,0.000000000],[0.018746003,0.009095718,0.183160424,0.010050260,0.000000000],[0.009277461,0.182896714,0.001911679,0.034113629,0.000000000],[0.233674193,0.009980139,0.037277643,0.010055624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|33 - 4V9F|1|9|A|47 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.016615310,0.020502196,0.014739411,0.020124104,0.000000000],[0.283439392,0.229531818,0.002418326,0.282844622,0.000000000],[0.025252980,0.002418326,0.026136650,0.010123545,0.000000000],[0.015802802,0.024193865,0.011325751,0.014530901,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|36 - 4V9F|1|9|A|47 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.136363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.318181818,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|A|34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.045454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.863636364,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|C|35
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // Initial node 4V9F|1|9|C|37 - 4V9F|1|9|C|46 from node 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [1] | Num Right Bases [4] | Left Index [5] | Right Index [9] | Norm Constant [0.530365125233084] // Cluster node 4V9F|1|9|C|37:4V9F|1|9|C|37 and 4V9F|1|9|G|43:4V9F|1|9|C|46
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.003503974,0.006283467,0.004028249,0.073040105,0.000000000],[0.052150337,0.024980872,0.620047911,0.035469147,0.000000000],[0.004073488,0.074613923,0.000767827,0.008622062,0.000000000],[0.073986997,0.004881977,0.009836416,0.003713248,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|37 - 4V9F|1|9|G|43 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.006847305,0.006847305,0.006847305,0.006847305,0.000000000],[0.006847305,0.006847305,0.125512130,0.006847305,0.000000000],[0.006847305,0.778625602,0.006847305,0.006847305,0.000000000],[0.006847305,0.006847305,0.006847305,0.006847305,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|G|43 - 4V9F|1|9|C|46 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.863636364,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4V9F|1|9|A|44
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.755319149,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.010638298,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.010638298,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.223404255,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4V9F|1|9|A|45
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_58103.11:
> IL_58103.11  4V9F U   33 A   47
UACCC*GAACA
> IL_58103.11  5NS3 A   34 U   48
ACCCC*GAACU
> IL_58103.11  9DFE U   34 A   48
UUCCC*GAACA
> IL_58103.11  8OI5 U   32 A   45
UCCCC*GAUCA
> IL_58103.11  8P9A U   32 A   45
UUCCC*GAUCA
> IL_58103.11  4WF9 U   32 A   46
UUCCC*GAACA
> IL_58103.11  5J7L A   34 U   48
ACCCC*GAACU
> IL_58103.11  7A0S A   36 U   50
ACCCC*GAACU
> IL_58103.11  1MJI A   34 U   48
ACCCC*GAACU