Alignment of IL_80093.1 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
4

3
7
4
I

8
5

4
9
5
I

10
6

5
11
6
I

12
7


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
4

8
19
3
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_80093.1_Instance_1 IL_80093.1_IL_4A1B_074_U1718_A1777UUAACGGCAGA
IL_80093.1_Sequence_1 IL_80093.1_IL_4A1B_074_U_1718_A_1777UUAAC*GGCAGAtrue100000.00
IL_80093.1_Instance_2 IL_80093.1_IL_1S72_056_C1570_G1627CGAACGCAUAG
IL_80093.1_Sequence_2 IL_80093.1_IL_1S72_056_C_1570_G_1627CGAAC*GCAUAGtrue97000.41

Conserved interactions between motif group positions in IL_80093.1:
1 2 s35 
1 10 cWW 
2 8 s35 
2 9 tSH 
2 10 s55 
3 4 s35 
3 8 tHH 
3 9 s55 
4 5 s35 
4 7 tHS 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s33 
8 9 s53 
9 10 s35 
8 3 6BPh
4 7 6BR
JAR3D SCFG/MRF model for IL_80093.1:
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 [10] // Initial node U1718 - A1777 from junction 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.009573432,0.018670696,0.010738592,0.199847452,0.000000000],[0.022636955,0.009050270,0.214230681,0.012151330,0.000000000],[0.010821283,0.200582138,0.002151860,0.023718468,0.000000000],[0.214249849,0.011785171,0.027717608,0.012074217,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [10] // Basepair U1718 - A1777 cWW 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.101728279,0.118577332,0.001225696,0.005836608,0.000000000],[0.102633356,0.107574724,0.001225696,0.001225696,0.000000000],[0.132373524,0.001225696,0.005938240,0.101953298,0.000000000],[0.209505519,0.106524945,0.001225696,0.001225696,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair U1719 - A1775 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.295197555,0.283041942,0.003523444,0.003492595,0.000000000],[0.069650800,0.003049065,0.065340104,0.030070705,0.000000000],[0.018952628,0.156448550,0.002248308,0.000775677,0.000000000],[0.018634804,0.048022471,0.000775677,0.000775677,0.000000000],[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 [3] | Right Index [8] // Basepair A1720 - C1774 tHH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.129506361,0.142111874,0.140738059,0.131659396,0.000000000],[0.126673089,0.112243512,0.001432729,0.126990143,0.000000000],[0.001432729,0.001432729,0.008529896,0.001432729,0.000000000],[0.008039397,0.001432729,0.064911900,0.001432729,0.000000000],[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 [4] | Right Index [7] // Basepair A1721 - G1773 tHS 
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 [5] | Right Index [6] // Basepair C1722 - G1772 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_80093.1:
> IL_80093.1 IL_4A1B_074 U 1718 A 1777
UUAAC*GGCAGA
> IL_80093.1 IL_1S72_056 C 1570 G 1627
CGAAC*GCAUAG