Alignment of IL_65137.1 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
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

6
13
6
I

14
7

7
15
7
I

16
8


17
7
I

18
7

8
19
6
I

20
6

9
21
3
I

22
2

10
23
2
I

24
2

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_65137.1_Instance_1 IL_65137.1_IL_1GID_011_C121_G200CAACAGCGACAUG
IL_65137.1_Sequence_1 IL_65137.1_IL_1GID_011_C121_G200CAACAGC*GACAUGtrue100000.00
IL_65137.1_Instance_2 IL_65137.1_IL_1GID_004_C121_G200CAACAGCGACAUG
IL_65137.1_Sequence_2 IL_65137.1_IL_1GID_004_C121_G200CAACAGC*GACAUGtrue100000.00

Conserved interactions between motif group positions in IL_65137.1:
1 12 cWW 
2 11 s53 
3 4 s35 
3 10 s33 
3 11 tWH 
4 5 perp 
4 6 s35 
4 10 tHW 
6 7 s35 
6 9 cWW 
7 8 cWW 
8 9 s35 
9 10 s35 
10 12 cSS 
11 12 s55 
JAR3D SCFG/MRF model for IL_65137.1:
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 [12] // Initial node C121 - G200 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000385733987058166880000000000000000000000000] | Num Left Bases [4] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.069027650754265] // Cluster node C121:C124 and C197:G200
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.023901948,0.030788172,0.006506405,0.054018837,0.000000000],[0.006506405,0.670248327,0.006506405,0.006506405,0.000000000],[0.026107257,0.029330674,0.029672622,0.027092263,0.000000000],[0.006506405,0.006506405,0.028934702,0.040866771,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C124 - C197 tHW 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.418144609,0.003985368,0.341751342,0.003985368,0.000000000],[0.031463906,0.014640658,0.022813077,0.003985368,0.000000000],[0.003985368,0.003985368,0.049366656,0.035560217,0.000000000],[0.019002964,0.003985368,0.023593614,0.019750751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A123 - A198 tWH 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C121 - G200 cWW 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.063042168,0.068409506,0.066609789,0.064659443,0.000000000],[0.065040058,0.066636573,0.091739532,0.062193072,0.000000000],[0.064213682,0.009354657,0.059985255,0.062705098,0.000000000],[0.063537723,0.059343905,0.069143067,0.063386474,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C197 - G200 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A122
Insertion    | Location [6] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 11, position 6 in cluster node
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 [5] | Right Index [9] // Initial node A125 - A196 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [9] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.045558309,0.014099396,0.342018043,0.016229361,0.000000000],[0.014438420,0.005788124,0.019549681,0.043692861,0.000000000],[0.375595066,0.019303593,0.003559872,0.015694806,0.000000000],[0.016257062,0.041075014,0.016050017,0.011090375,0.000000000],[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 [6] | Right Index [9] // Basepair G126 - A196 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 [7] | Right Index [8] // Basepair C127 - G195 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_65137.1:
> IL_65137.1 IL_1GID_011 C  121 G  200
CAACAGC*GACAUG
> IL_65137.1 IL_1GID_004 C  121 G  200
CAACAGC*GACAUG