Alignment of IL_53635.3 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
5

2
5
5
I

6
6

3
7
6
I

8
7

4
9
7
I

10
8

5
11
8
I

12
9


13
8
I

14
8

6
15
7
I

16
7

7
17
6
I

18
6

8
19
5
I

20
5

9
21
4
I

22
3

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_53635.3_Instance_1 IL_53635.3_IL_3V2F_018_G674_C806GAAACGAGAUAGC
IL_53635.3_Sequence_1 IL_53635.3_IL_3V2F_018_G674_C806GAAAC*GAGAUAGCtrue100000.00
IL_53635.3_Instance_2 IL_53635.3_IL_2QBG_021_G674_C806GAAACGAGAUAGC
IL_53635.3_Sequence_2 IL_53635.3_IL_2QBG_021_G674_C806GAAAC*GAGAUAGCtrue100000.00
IL_53635.3_Instance_3 IL_53635.3_IL_1S72_025_G765_C899GAAUCGCAACAGC
IL_53635.3_Sequence_3 IL_53635.3_IL_1S72_025_G765_C899GAAUC*GCAACAGCtrue82003.62
IL_53635.3_Instance_4 IL_53635.3_IL_4A1B_035_G830_C963GAAAGCUAGUAGC
IL_53635.3_Sequence_4 IL_53635.3_IL_4A1B_035_G830_C963GAAAG*CUAGUAGCtrue84003.11
IL_53635.3_Instance_5 IL_53635.3_IL_4IOA_014_G687_C819GAAACGAGAUAGC
IL_53635.3_Sequence_5 IL_53635.3_IL_4IOA_014_G687_C819GAAAC*GAGAUAGCtrue100000.00
IL_53635.3_Instance_6 IL_53635.3_IL_3U5H_029_G805_C938GAAAGCUAGUAGC
IL_53635.3_Sequence_6 IL_53635.3_IL_3U5H_029_G805_C938GAAAG*CUAGUAGCtrue84003.11

Conserved interactions between motif group positions in IL_53635.3:
1 10 s33 
1 11 cWW 
2 3 s35 
2 9 tHW 
2 10 s55 
3 8 tHW 
4 5 s35 
4 7 tWW 
4 8 s55 
5 6 cWW 
6 7 s33 
7 8 s55 
8 9 s35 
9 10 s35 
10 2 6BR
JAR3D SCFG/MRF model for IL_53635.3:
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 G674 - C806 from junction 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009810372,0.019985697,0.011358953,0.186173951,0.000000000],[0.016552873,0.008089349,0.200518679,0.012762933,0.000000000],[0.011215968,0.263443051,0.002068393,0.026530626,0.000000000],[0.185098881,0.013397366,0.022885515,0.010107394,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Left Index [1] | Right Index [11] // Basepair G674 - C806 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.953125000,0.015625000,0.015625000,0.015625000,0.000000000] | Position [2] | Left Index [2] | Right Index [10] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [2] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.024010722,0.093152721,0.004771130,0.487955535,0.000000000],[0.004771130,0.038171791,0.004771130,0.004771130,0.000000000],[0.044022502,0.066387877,0.053871957,0.055814147,0.000000000],[0.004771130,0.004771130,0.024540096,0.083445872,0.000000000],[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 [2] | Right Index [9] // Basepair A675 - U803 tHW 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.414957834,0.027524172,0.079529796,0.016623519,0.000000000],[0.003486342,0.012807437,0.003486342,0.003486342,0.000000000],[0.298959150,0.019956551,0.043185240,0.020639353,0.000000000],[0.003486342,0.003486342,0.031107565,0.017277672,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.437500000,0.062500000,0.437500000,0.062500000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A676 - A802 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.360594839,0.031200513,0.003322930,0.091785179,0.000000000],[0.031239901,0.012871807,0.010108516,0.012694969,0.000000000],[0.003322930,0.010103019,0.313906749,0.018183499,0.000000000],[0.015745234,0.050716942,0.018200359,0.016002616,0.000000000],[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 [4] | Right Index [7] // Basepair A677 - A800 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009704981,0.017699381,0.011265142,0.185482208,0.000000000],[0.018844119,0.008192545,0.242496164,0.013187696,0.000000000],[0.011312823,0.221520521,0.002068672,0.024103639,0.000000000],[0.185840710,0.012976132,0.025319168,0.009986100,0.000000000],[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 [5] | Right Index [6] // Basepair C678 - G799 cWW 
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_53635.3:
> IL_53635.3 IL_3V2F_018 G  674 C  806
GAAAC*GAGAUAGC
> IL_53635.3 IL_2QBG_021 G  674 C  806
GAAAC*GAGAUAGC
> IL_53635.3 IL_1S72_025 G  765 C  899
GAAUC*GCAACAGC
> IL_53635.3 IL_4A1B_035 G  830 C  963
GAAAG*CUAGUAGC
> IL_53635.3 IL_4IOA_014 G  687 C  819
GAAAC*GAGAUAGC
> IL_53635.3 IL_3U5H_029 G  805 C  938
GAAAG*CUAGUAGC