Alignment of IL_77263.2 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
3

3
7
3
I

8
3

4
9
4
I

10
5

5
11
5
I

12
6

6
13
6
I

14
7


15
6
I

16
6

7
17
5
I

18
5

8
19
4
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_77263.2_Instance_1 IL_77263.2_IL_3SIU_001_C33_G50CAAUGAGUGAG
IL_77263.2_Sequence_1 IL_77263.2_IL_3SIU_001_C33_G50CAAUGAG*UGAGtrue100000.00
IL_77263.2_Instance_2 IL_77263.2_IL_2OZB_002_C28_G45CAAUGAGCGAG
IL_77263.2_Sequence_2 IL_77263.2_IL_2OZB_002_C28_G45CAAUGAG*CGAGtrue98000.31
IL_77263.2_Instance_3 IL_77263.2_IL_3SIV_003_C33_G50CAAUGAGUGAG
IL_77263.2_Sequence_3 IL_77263.2_IL_3SIV_003_C33_G50CAAUGAG*UGAGtrue100000.00
IL_77263.2_Instance_4 IL_77263.2_IL_3SIV_001_C33_G50CAAUGAGUGAG
IL_77263.2_Sequence_4 IL_77263.2_IL_3SIV_001_C33_G50CAAUGAG*UGAGtrue100000.00
IL_77263.2_Instance_5 IL_77263.2_IL_1E7K_002_C28_G45CAAUGAGCGAG
IL_77263.2_Sequence_5 IL_77263.2_IL_1E7K_002_C28_G45CAAUGAG*CGAGtrue98000.31
IL_77263.2_Instance_6 IL_77263.2_IL_4LCK_001_C6_G97CGAUGAGCGAG
IL_77263.2_Sequence_6 IL_77263.2_IL_4LCK_001_C6_G97CGAUGAG*CGAGtrue90001.54

Conserved interactions between motif group positions in IL_77263.2:
1 2 s35 
1 10 cWW 
2 9 tSS 
2 10 s55 
3 4 s35 
3 9 s33 
4 8 s33 
4 9 tSH 
5 6 s35 
5 8 tHS 
5 9 s55 
6 7 cWW 
6 8 s55 
7 8 s35 
9 10 perp 
8 4 6BR
9 4 6BR
10 5 2BR
4 8 6BR
5 8 6BR
3 9 6BR
JAR3D SCFG/MRF model for IL_77263.2:
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 [10] // Initial node C33 - G50 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004717578,0.008091894,0.027414702,0.090485831,0.000000000],[0.009770034,0.004029345,0.562172037,0.006549320,0.000000000],[0.005552839,0.098023820,0.005055683,0.011187614,0.000000000],[0.091011380,0.006239176,0.064847658,0.004851089,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair C33 - G50 cWW 
ClusterNode  | Deletion Probability [0.0000000000031115] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [9] | Norm Constant [0.416274113910334] // Cluster node A34:G37 and A49:A49
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.528849073,0.083541625,0.076461802,0.077107477,0.000000000],[0.005827225,0.001165445,0.001165445,0.001165445,0.000000000],[0.153166296,0.026129033,0.026624910,0.009472662,0.000000000],[0.005827225,0.001165445,0.001165445,0.001165445,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A34 - A49 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.071085104,0.082858788,0.000856485,0.004078472,0.000000000],[0.071717548,0.075170449,0.000856485,0.000856485,0.000000000],[0.311861171,0.002552574,0.012366685,0.212322902,0.000000000],[0.077266991,0.074436891,0.000856485,0.000856485,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G37 - A49 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.953125000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A35
Insertion    | Location [2] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.052788444,0.053258103,0.374620487,0.057379170,0.000000000],[0.061531689,0.055822259,0.003180167,0.055277512,0.000000000],[0.000636033,0.000636033,0.015407242,0.000636033,0.000000000],[0.003028710,0.000636033,0.264526051,0.000636033,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A38 - G48 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012844072,0.159282715,0.013171233,0.114580161,0.000000000],[0.015240908,0.009601556,0.118644620,0.013806282,0.000000000],[0.012933937,0.153035139,0.002695858,0.207733360,0.000000000],[0.110794989,0.014924503,0.018737671,0.021972996,0.000000000],[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 [6] | Right Index [7] // Basepair G39 - U47 cWW 
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_77263.2:
> IL_77263.2 IL_3SIU_001 C   33 G   50
CAAUGAG*UGAG
> IL_77263.2 IL_2OZB_002 C   28 G   45
CAAUGAG*CGAG
> IL_77263.2 IL_3SIV_003 C   33 G   50
CAAUGAG*UGAG
> IL_77263.2 IL_3SIV_001 C   33 G   50
CAAUGAG*UGAG
> IL_77263.2 IL_1E7K_002 C   28 G   45
CAAUGAG*CGAG
> IL_77263.2 IL_4LCK_001 C    6 G   97
CGAUGAG*CGAG