Alignment of IL_21254.1 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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
4
I

12
5


13
4
I

14
3

6
15
3
I

16
3

7
17
3
I

18
3

8
19
3
I

20
3

9
21
3
I

22
3

10
23
3
I

24
3

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_21254.1_Instance_1 IL_21254.1_IL_1FJG_011_C242_G284CAUCAGCGACGACG
IL_21254.1_Sequence_1 IL_21254.1_IL_1FJG_011_C242_G284CAUCAG*CGACGACGtrue100000.00

Conserved interactions between motif group positions in IL_21254.1:
1 3 s35 
1 12 cWW 
2 3 s53 
2 4 s35 
2 9 s33 
2 10 tWH 
2 11 s55 
3 11 cWW 
3 12 s55 
4 8 s35 
4 9 tHS 
4 10 s55 
5 6 cWW 
5 7 s55 
5 10 tSS 
6 10 cSS 
10 11 s35 
11 12 s35 
11 10 7BPh
2 4 2BR
10 4 6BR
4 7 6BR
JAR3D SCFG/MRF model for IL_21254.1:
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 C242 - G284 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 [12] // Basepair C242 - G284 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000232685345145757480000000000000000] | Num Left Bases [4] | Num Right Bases [6] | Left Index [2] | Right Index [11] | Norm Constant [0.028977363705361] // Cluster node A243:G247 and C277:C283
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G247 - C277 cWW 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.190666382,0.192362741,0.239629664,0.207247608,0.000000000],[0.044449215,0.040324841,0.000459457,0.039931327,0.000000000],[0.000459457,0.000459457,0.002225974,0.000459457,0.000000000],[0.002187877,0.000459457,0.038217626,0.000459457,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A246 - G281 tHS 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.821017114,0.001622232,0.139108884,0.001622232,0.000000000],[0.012807291,0.001191887,0.001857199,0.000324446,0.000000000],[0.001622232,0.000324446,0.004018911,0.002894936,0.000000000],[0.007735101,0.000324446,0.001920742,0.001607897,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A243 - A282 tWH 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.027712781,0.006212429,0.007326944,0.006291967,0.000000000],[0.006675544,0.001335109,0.001335109,0.001335109,0.000000000],[0.677455366,0.118763300,0.120038767,0.014836705,0.000000000],[0.006675544,0.001335109,0.001335109,0.001335109,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G247 - A282 tSS 
Interaction  | Interacting Bases [2,10] | Pair Probability [[0.001230782,0.029830503,0.001880084,0.005330434,0.000000000],[0.006116993,0.871448255,0.004904624,0.003243165,0.000000000],[0.002001172,0.033694550,0.001230782,0.004115946,0.000000000],[0.005447712,0.018814483,0.005603215,0.005107300,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C245 - C283 cWW 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.152585019,0.031075256,0.030154202,0.030666816,0.000000000],[0.184000410,0.031248979,0.003826899,0.028728496,0.000000000],[0.162621226,0.033023087,0.029991440,0.033218374,0.000000000],[0.157692540,0.030743306,0.029504872,0.030919078,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C277 - A282 cSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G278
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A279
Insertion    | Location [1] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
Insertion    | Location [7] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 8, position 7 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 [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_21254.1:
> IL_21254.1 IL_1FJG_011 C  242 G  284
CAUCAG*CGACGACG