Alignment of IL_70173.1 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
4
I

6
7

3
7
7
I

8
8


9
7
I

10
7

4
11
6
I

12
5

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_70173.1_Instance_1 IL_70173.1_IL_4M4O_004_G26_C41GAGCAC
IL_70173.1_Sequence_1 IL_70173.1_IL_4M4O_004_G26_C41GAG*CACtrue100000.00
IL_70173.1_Instance_2 IL_70173.1_IL_4M6D_013_G26_C41GAGCAC
IL_70173.1_Sequence_2 IL_70173.1_IL_4M6D_013_G26_C41GAG*CACtrue100000.00
IL_70173.1_Instance_3 IL_70173.1_IL_3U5H_085_C2333_G1906CUGUAGUCGG
IL_70173.1_Sequence_3 IL_70173.1_IL_3U5H_085_C_2333_G_1906CUGU*AGUCGGtrue31006.52
IL_70173.1_Instance_4 IL_70173.1_IL_4A1B_081_C2328_G1930CUGUAGUCGG
IL_70173.1_Sequence_4 IL_70173.1_IL_4A1B_081_C_2328_G_1930CUGU*AGUCGGtrue31006.52
IL_70173.1_Instance_5 IL_70173.1_IL_3BNL_002_C6_G18CACGAAG
IL_70173.1_Sequence_5 IL_70173.1_IL_3BNL_002_C6_G18CAC*GAAGtrue76002.30
IL_70173.1_Instance_6 IL_70173.1_IL_3U5F_093_U1688_G1713UAGCAG
IL_70173.1_Sequence_6 IL_70173.1_IL_3U5F_093_U_1688_G_1713UAG*CAGtrue92000.80

Conserved interactions between motif group positions in IL_70173.1:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
3 4 cWW 
JAR3D SCFG/MRF model for IL_70173.1:
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 [6] // Initial node G26 - C41 from junction 
BasepairNode | Deletion Probability [0.0000001161691144] | Pair Probability [[0.010184077,0.017311551,0.011890069,0.160839123,0.000000000],[0.066348660,0.009394494,0.205839722,0.013755405,0.000000000],[0.011970373,0.194354531,0.002289699,0.022772678,0.000000000],[0.162124296,0.013376844,0.086913343,0.010635134,0.000000000],[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 [0.659069065,0.005492242,0.003020733,0.329534532,0.002746121,0.000137306] | Right Letter Distribution [0.062500000,0.312500000,0.312500000,0.312500000,0.000000000] | Left Index [1] | Right Index [6] // Basepair G26 - C41 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left
InitialNode  | Left Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Left Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.562500000,0.062500000,0.312500000,0.062500000,0.000000000] | Position [2] | Left Index [3] | Right Index [5] // 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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009437919,0.019210905,0.010698678,0.190434945,0.000000000],[0.019466633,0.008476484,0.206354808,0.011943313,0.000000000],[0.010656397,0.226970317,0.002069833,0.024665910,0.000000000],[0.211536085,0.012131395,0.024801198,0.011145179,0.000000000],[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 G28 - C39 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_70173.1:
> IL_70173.1 IL_4M4O_004 G   26 C   41
GAG*CAC
> IL_70173.1 IL_4M6D_013 G   26 C   41
GAG*CAC
> IL_70173.1 IL_3U5H_085 C 2333 G 1906
CUGU*AGUCGG
> IL_70173.1 IL_4A1B_081 C 2328 G 1930
CUGU*AGUCGG
> IL_70173.1 IL_3BNL_002 C    6 G   18
CAC*GAAG
> IL_70173.1 IL_3U5F_093 U 1688 G 1713
UAG*CAG