Alignment of IL_65594.1 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
5

4
9
5
I

10
6

5
11
6
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12
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6
13
7
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14
8

7
15
8
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16
9

8
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9
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18
10


19
9
I

20
9

9
21
8
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22
8

10
23
7
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24
6

11
25
5
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26
5

12
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4
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28
4

13
29
3
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30
3

14
31
2
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32
2

15
33
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_65594.1_Instance_1 IL_65594.1,IL_8P9A_235,C82_G103CUUAGUAAUGAAGCG
IL_65594.1_Sequence_1 IL_65594.18P9A_C82_G103CUUAGUAA*UGAAGCGtrue98000.39
IL_65594.1_Instance_2 IL_65594.1,IL_8CRE_006,C81_G102CUCAGUAGUGAAGCG
IL_65594.1_Sequence_2 IL_65594.18CRE_C81_G102CUCAGUAG*UGAAGCGtrue100000.00

Conserved interactions between motif group positions in IL_65594.1:
1 2 s35 
1 15 cWW 
2 3 s35 
2 14 tSH 
3 4 s33 
3 13 tSW 
4 6 s55 
4 11 s53 
4 12 tHH 
5 6 cSH 
5 10 s33 
6 7 s35 
6 10 s33 
6 11 tWH 
7 8 s35 
7 10 tHS 
7 11 s55 
8 9 cWW 
8 10 s55 
9 10 s35 
11 12 s35 
12 13 s33 
13 14 s55 
14 15 s35 
10 6 6BPh
5 11 6BPh
4 12 6BPh
13 13 2BPh
7 10 6BR
JAR3D SCFG/MRF model for IL_65594.1:
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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [15] // Basepair C82 - G103 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.131981958,0.095112703,0.001468808,0.006957326,0.000000000],[0.134240277,0.125867935,0.001468808,0.001468808,0.000000000],[0.128533182,0.001468808,0.007622310,0.058620191,0.000000000],[0.135762660,0.166488612,0.001468808,0.001468808,0.000000000],[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 [14] // Basepair U83 - C102 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.004557124,0.004268932,0.008538630,0.027273599,0.000000000],[0.004496666,0.003253131,0.471084431,0.004658177,0.000000000],[0.005110728,0.012541716,0.008538630,0.003400000,0.000000000],[0.003463007,0.003379219,0.410925065,0.024510943,0.000000000],[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 [13] // Basepair U84 - G101 tSW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.431873884,0.331200569,0.019765828,0.020165858,0.000000000],[0.051813191,0.000588951,0.050208540,0.005596268,0.000000000],[0.002936349,0.049566880,0.001470022,0.000588951,0.000000000],[0.004000200,0.029046605,0.000588951,0.000588951,0.000000000],[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 [12] // Basepair A85 - A100 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.262628314674858] // Cluster node 8P9A|1|AR|G|86:8P9A|1|AR|U|87 and 8P9A|1|AR|A|99:8P9A|1|AR|A|99
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|87 - 8P9A|1|AR|A|99 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.031106004,0.031695591,0.001742722,0.030975664,0.000000000],[0.023222664,0.034996963,0.000385868,0.031040601,0.000000000],[0.190241664,0.002701077,0.232062401,0.289715574,0.000000000],[0.031588643,0.031399012,0.000385868,0.036739684,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|86 - 8P9A|1|AR|U|87 cSH 
InitialNode  | 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 [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.044022640,0.386803555,0.048778633,0.000000000],[0.046260217,0.046153098,0.003671957,0.045903932,0.000000000],[0.000524565,0.000524565,0.017951032,0.000524565,0.000000000],[0.002472278,0.000524565,0.311661837,0.000524565,0.000000000],[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 [7] | Right Index [10] // Basepair A88 - G98 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012561376,0.159448752,0.012116000,0.154152905,0.000000000],[0.015620465,0.011184829,0.115298895,0.012381896,0.000000000],[0.011952985,0.119123056,0.002642771,0.198630374,0.000000000],[0.116300976,0.013381394,0.018705281,0.026498044,0.000000000],[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 [8] | Right Index [9] // Basepair A89 - U97 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_65594.1:
> IL_65594.1  8P9A C   82 G  103
CUUAGUAA*UGAAGCG
> IL_65594.1  8CRE C   81 G  102
CUCAGUAG*UGAAGCG