Alignment of IL_76486.1 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
I

12
6

6
13
7
I

14
8

7
15
8
I

16
9

8
17
9
I

18
10


19
9
I

20
9

9
21
8
I

22
8

10
23
7
I

24
6

11
25
5
I

26
5

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_76486.1_Instance_1 IL_76486.1_IL_3U5H_006_C82_G103CUUAGUAAUGAAGCG
IL_76486.1_Sequence_1 IL_76486.1_IL_3U5H_006_C82_G103CUUAGUAA*UGAAGCGtrue100000.00

Conserved interactions between motif group positions in IL_76486.1:
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 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
3 4 7BR
7 10 6BR
JAR3D SCFG/MRF model for IL_76486.1:
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 C82 - G103 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[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 C82 - G103 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.133633771,0.127486748,0.001506190,0.007324744,0.000000000],[0.135810798,0.130305286,0.001506190,0.001506190,0.000000000],[0.130902608,0.001506190,0.007522744,0.018755504,0.000000000],[0.138700667,0.160519989,0.001506190,0.001506190,0.000000000],[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 U83 - C102 tSH 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.001889513,0.001111336,0.001593034,0.013225307,0.000000000],[0.001554591,0.001207481,0.135152057,0.002075013,0.000000000],[0.001268155,0.015077930,0.001593034,0.001383172,0.000000000],[0.005493426,0.005490697,0.806417865,0.005467389,0.000000000],[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 [3] | Right Index [13] // Basepair U84 - G101 tSW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.557926848,0.110624637,0.027357914,0.027399489,0.000000000],[0.010110700,0.000782894,0.067304067,0.055610500,0.000000000],[0.004890903,0.064961568,0.001917995,0.000782894,0.000000000],[0.004810890,0.063952913,0.000782894,0.000782894,0.000000000],[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 [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 [0.460751978306534] // Cluster node G86:U87 and A99:A99
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.026228946,0.005500826,0.026982756,0.005500826,0.000000000],[0.054639536,0.045670107,0.036513624,0.005500826,0.000000000],[0.005500826,0.005500826,0.064376936,0.025659745,0.000000000],[0.559983562,0.005500826,0.067861159,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U87 - A99 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.055679592,0.057359966,0.003128224,0.002588218,0.000000000],[0.053859163,0.062562107,0.000665346,0.063050334,0.000000000],[0.038079735,0.020824015,0.042566873,0.475642955,0.000000000],[0.004791044,0.055793641,0.000665346,0.062743443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G86 - U87 cSH 
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 [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044149057,0.044541851,0.382258874,0.047988462,0.000000000],[0.051461378,0.046686356,0.003723579,0.046230763,0.000000000],[0.000531940,0.000531940,0.018039957,0.000531940,0.000000000],[0.002533030,0.000531940,0.309726994,0.000531940,0.000000000],[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 [7] | Right Index [10] // Basepair A88 - G98 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[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_76486.1:
> IL_76486.1 IL_3U5H_006 C   82 G  103
CUUAGUAA*UGAAGCG