Alignment of IL_16415.2 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
7

3
7
7
I

8
8

4
9
8
I

10
8

5
11
8
I

12
8

6
13
9
I

14
10


15
9
I

16
8

7
17
8
I

18
8

8
19
8
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20
8

9
21
8
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22
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10
23
8
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24
8

11
25
7
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26
7

12
27
6
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28
5

13
29
2
I

30
2

14
31
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_16415.2_Instance_1 IL_16415.2_IL_1FJG_031_G683_C707GAGUAGCGCAGAUAC
IL_16415.2_Sequence_1 IL_16415.2_IL_1FJG_031_G683_C707GAGUAG*CGCAGAUACtrue100000.00
IL_16415.2_Instance_2 IL_16415.2_IL_4BPP_047_A872_U896AGUCAGCUUGGAUUU
IL_16415.2_Sequence_2 IL_16415.2_IL_4BPP_047_A872_U896AGUCAG*CUUGGAUUUtrue91001.79
IL_16415.2_Instance_3 IL_16415.2_IL_3V2F_084_G2154_C2137GGGGAGCUGUGAACC
IL_16415.2_Sequence_3 IL_16415.2_IL_3V2F_084_G_2154_C_2137GGGGAG*CUGUGAACCtrue96000.80

Conserved interactions between motif group positions in IL_16415.2:
1 2 s35 
1 14 cWW 
2 3 s35 
2 14 s55 
3 4 s35 
3 12 tSH 
3 13 s55 
4 10 s33 
4 11 tWH 
5 8 tSS 
5 9 s35 
5 10 tHS 
5 11 s55 
6 7 cWW 
6 8 s55 
6 11 tSS 
7 8 s35 
9 10 s55 
11 12 s35 
12 13 s35 
13 14 s35 
3 11 6BPh
5 8 6BR
JAR3D SCFG/MRF model for IL_16415.2:
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 [14] // Initial node G683 - C707 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009784429,0.021777989,0.011031390,0.208347691,0.000000000],[0.017985926,0.008620950,0.201027673,0.012148861,0.000000000],[0.010927772,0.225150163,0.002128171,0.027374013,0.000000000],[0.195241385,0.012608128,0.023487298,0.012358162,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G683 - C707 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [13] // 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 [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.300000000,0.100000000,0.300000000,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.024365078,0.049254635,0.000551847,0.002964234,0.000000000],[0.024333849,0.025191930,0.000551847,0.000551847,0.000000000],[0.360272004,0.003862929,0.022477458,0.366756534,0.000000000],[0.036455331,0.025365961,0.000551847,0.056492670,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // Basepair G685 - U705 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000001936518681344305600000000000000000000000] | Num Left Bases [3] | Num Right Bases [5] | Left Index [4] | Right Index [11] | Norm Constant [0.059289822346423] // Cluster node U686:G688 and C699:A704
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G688 - C699 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.178334863,0.194159396,0.211510727,0.269655199,0.000000000],[0.002162307,0.002162307,0.002162307,0.002162307,0.000000000],[0.010959123,0.011829242,0.016274252,0.089978741,0.000000000],[0.002162307,0.002162307,0.002162307,0.002162307,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A687 - G700 tSS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.186964122,0.188627543,0.254394136,0.203223383,0.000000000],[0.043586124,0.039541834,0.000450536,0.039155962,0.000000000],[0.000450536,0.000450536,0.002182752,0.000450536,0.000000000],[0.002145394,0.000450536,0.037475536,0.000450536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A687 - G703 tHS 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.021610380,0.003754531,0.079044280,0.003754531,0.000000000],[0.153817650,0.026937290,0.127005017,0.003754531,0.000000000],[0.059695354,0.003754531,0.038161270,0.024230069,0.000000000],[0.278346563,0.003754531,0.037364260,0.135015212,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U686 - A704 tWH 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.012109700,0.013573278,0.016008335,0.013747056,0.000000000],[0.002917024,0.002917024,0.002917024,0.002917024,0.000000000],[0.367060650,0.259480989,0.262267704,0.032416099,0.000000000],[0.002917024,0.002917024,0.002917024,0.002917024,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G688 - A704 tSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion C701
Insertion    | Location [6] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000]// Insertion after nucleotide 9, position 6 in cluster node
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 [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_16415.2:
> IL_16415.2 IL_1FJG_031 G  683 C  707
GAGUAG*CGCAGAUAC
> IL_16415.2 IL_4BPP_047 A  872 U  896
AGUCAG*CUUGGAUUU
> IL_16415.2 IL_3V2F_084 G 2154 C 2137
GGGGAG*CUGUGAACC