Alignment of IL_77014.1 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
9
I

12
9

6
13
9
I

14
9

7
15
9
I

16
9

8
17
10
I

18
11


19
10
I

20
9

9
21
9
I

22
9

10
23
2
I

24
2

11
25
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_77014.1_Instance_1 IL_77014.1_IL_3P59_003_G51_C112GGAACUACGCC
IL_77014.1_Sequence_1 IL_77014.1_IL_3P59_003_G51_C112GGAACUAC*GCCtrue100000.00

Conserved interactions between motif group positions in IL_77014.1:
1 2 s35 
1 11 cWW 
2 3 s35 
2 11 s55 
3 4 s35 
5 7 cSH 
5 9 tWH 
6 7 s35 
7 8 s35 
7 10 cWW 
8 9 cWW 
9 10 s35 
11 9 7BPh
6 5 7BR
JAR3D SCFG/MRF model for IL_77014.1:
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 [11] // Initial node G51 - C112 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003991852,0.056925429,0.004621971,0.075754404,0.000000000],[0.006735384,0.023040960,0.081591292,0.005193253,0.000000000],[0.004563791,0.599043046,0.000841632,0.010795344,0.000000000],[0.075316957,0.038159832,0.009312144,0.004112711,0.000000000],[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 [11] // Basepair G51 - C112 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000015625000000000003000000000000000000000000000000] | Num Left Bases [4] | Num Right Bases [2] | Left Index [5] | Right Index [10] | Norm Constant [0.016946694239089] // Cluster node C55:C58 and G110:C111
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.017042123,0.002977202,0.037605848,0.002977202,0.000000000],[0.276030134,0.013421133,0.307621142,0.002977202,0.000000000],[0.002977202,0.002977202,0.014455549,0.023565365,0.000000000],[0.019762200,0.002977202,0.013381459,0.259251838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C55 - G110 tWH 
Interaction  | Interacting Bases [4,5] | 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]] // Cluster Interaction C58 - G110 cWW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.014465575,0.343792072,0.013542226,0.037981708,0.000000000],[0.013601003,0.011560757,0.026720538,0.013366648,0.000000000],[0.013224246,0.032261987,0.003338911,0.299980183,0.000000000],[0.031215838,0.014829276,0.013994275,0.116124756,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A57 - C111 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.121142655,0.120842989,0.006476604,0.005755261,0.000000000],[0.144971527,0.110518240,0.001350705,0.112517076,0.000000000],[0.006512780,0.006422996,0.011124298,0.109338445,0.000000000],[0.016481658,0.116826263,0.001350705,0.108367796,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C55 - A57 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U56
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 [9] | Right Index [8] // New Initial node after Cluster
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_77014.1:
> IL_77014.1 IL_3P59_003 G   51 C  112
GGAACUAC*GCC