Alignment of IL_21333.2 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
3
I

6
4

3
7
4
I

8
5

4
9
5
I

10
6


11
5
I

12
5

5
13
4
I

14
4

6
15
3
I

16
3

7
17
2
I

18
2

8
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_21333.2_Instance_1 IL_21333.2_IL_3V2F_054_C1437_G1555CUAGCGAAG
IL_21333.2_Sequence_1 IL_21333.2_IL_3V2F_054_C_1437_G_1555CUAG*CGAAGtrue100000.00
IL_21333.2_Instance_2 IL_21333.2_IL_3V2F_011_A357_U284AUAGCGAAU
IL_21333.2_Sequence_2 IL_21333.2_IL_3V2F_011_A357_U284AUAG*CGAAUtrue99000.09
IL_21333.2_Instance_3 IL_21333.2_IL_1LNG_002_G223_C198GUAGCGAACCC
IL_21333.2_Sequence_3 IL_21333.2_IL_1LNG_002_G223_C198GUAG*CGAACCCtrue76002.80
IL_21333.2_Instance_4 IL_21333.2_IL_4IOA_055_C1451_G1571CUAUAAACG
IL_21333.2_Sequence_4 IL_21333.2_IL_4IOA_055_C_1451_G_1571CUAU*AAACGtrue97000.34

Conserved interactions between motif group positions in IL_21333.2:
1 2 s35 
1 8 cWW 
2 3 s35 
2 6 s33 
2 7 tWH 
2 8 s55 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
3 6 6BR
JAR3D SCFG/MRF model for IL_21333.2:
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 [8] // Initial node C1437 - G1555 from junction 
BasepairNode | Deletion Probability [0.0000000085968736] | Pair Probability [[0.009686956,0.019521236,0.011016627,0.204071877,0.000000000],[0.019329018,0.008543656,0.222887911,0.012600826,0.000000000],[0.011048977,0.211935094,0.002108037,0.025238064,0.000000000],[0.192754738,0.012456923,0.025137840,0.011662222,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.009140768,0.731261426,0.012187690,0.244210847,0.003046923,0.000152346] | Right Letter Distribution [0.437500000,0.437500000,0.062500000,0.062500000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C1437 - G1555 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.025472342,0.005342148,0.026204408,0.005342148,0.000000000],[0.053063396,0.044352700,0.035460347,0.005342148,0.000000000],[0.005342148,0.005342148,0.062519909,0.024919560,0.000000000],[0.572676343,0.005342148,0.065903626,0.057374481,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U1438 - A1553 tWH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.130969856,0.120901106,0.160425389,0.125458163,0.000000000],[0.127242150,0.102549889,0.001382179,0.120832807,0.000000000],[0.001382179,0.001382179,0.008196369,0.001382179,0.000000000],[0.007812668,0.001382179,0.087318529,0.001382179,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A1439 - G1552 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009734462,0.020214697,0.011090593,0.193143617,0.000000000],[0.018660673,0.008521127,0.200813940,0.012300663,0.000000000],[0.010985401,0.234217224,0.002109217,0.026079210,0.000000000],[0.203918224,0.012767771,0.024324928,0.011118254,0.000000000],[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 [4] | Right Index [5] // Basepair G1440 - C1551 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_21333.2:
> IL_21333.2 IL_3V2F_054 C 1437 G 1555
CUAG*CGAAG
> IL_21333.2 IL_3V2F_011 A  357 U  284
AUAG*CGAAU
> IL_21333.2 IL_1LNG_002 G  223 C  198
GUAG*CGAACCC
> IL_21333.2 IL_4IOA_055 C 1451 G 1571
CUAU*AAACG