Alignment of IL_86357.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_86357.3
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


9
4
I

10
4

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_86357.3_Instance_1 IL_86357.3_IL_3U5H_083_A1895_U2340AAGCCU
IL_86357.3_Sequence_1 IL_86357.3_IL_3U5H_083_A_1895_U_2340AAG*CCUtrue100000.00
IL_86357.3_Instance_2 IL_86357.3_IL_1S72_060_U1741_A2038UAGCCA
IL_86357.3_Sequence_2 IL_86357.3_IL_1S72_060_U_1741_A_2038UAG*CCAtrue99000.05
IL_86357.3_Instance_3 IL_86357.3_IL_4A1B_079_A1919_U2335AAGCCU
IL_86357.3_Sequence_3 IL_86357.3_IL_4A1B_079_A_1919_U_2335AAG*CCUtrue100000.00
IL_86357.3_Instance_4 IL_86357.3_IL_2QBG_063_G1663_C1997GAAUCC
IL_86357.3_Sequence_4 IL_86357.3_IL_2QBG_063_G_1663_C_1997GAA*UCCtrue99000.13
IL_86357.3_Instance_5 IL_86357.3_IL_3V2F_062_C1663_G1997CAAUCG
IL_86357.3_Sequence_5 IL_86357.3_IL_3V2F_062_C_1663_G_1997CAA*UCGtrue99000.13

Conserved interactions between motif group positions in IL_86357.3:
1 6 cWW 
2 3 s35 
2 5 tWW 
3 4 cWW 
4 5 s33 
5 6 perp 
JAR3D SCFG/MRF model for IL_86357.3:
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 [6] // Initial node A1895 - U2340 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009295351,0.020785081,0.010277952,0.217760832,0.000000000],[0.019941766,0.008764932,0.204139468,0.011291914,0.000000000],[0.010274719,0.204355555,0.002088457,0.025369463,0.000000000],[0.206675622,0.011305972,0.024556092,0.013116825,0.000000000],[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 [6] // Basepair A1895 - U2340 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.032853642,0.397518223,0.003498992,0.039114777,0.000000000],[0.016637424,0.016275544,0.010646670,0.016012148,0.000000000],[0.003498992,0.013571742,0.038322192,0.323133304,0.000000000],[0.016476222,0.015549427,0.015692946,0.041197755,0.000000000],[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 [5] // Basepair A1896 - C2339 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009536910,0.021600597,0.010692095,0.215284636,0.000000000],[0.017829900,0.008514812,0.196152613,0.011724048,0.000000000],[0.010598992,0.228986356,0.002087543,0.026866464,0.000000000],[0.192454657,0.012136575,0.023027210,0.012506591,0.000000000],[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 [3] | Right Index [4] // Basepair G1897 - C2338 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_86357.3:
> IL_86357.3 IL_3U5H_083 A 1895 U 2340
AAG*CCU
> IL_86357.3 IL_1S72_060 U 1741 A 2038
UAG*CCA
> IL_86357.3 IL_4A1B_079 A 1919 U 2335
AAG*CCU
> IL_86357.3 IL_2QBG_063 G 1663 C 1997
GAA*UCC
> IL_86357.3 IL_3V2F_062 C 1663 G 1997
CAA*UCG