Alignment of IL_82683.2 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
11

5
11
11
I

12
12


13
11
I

14
11

6
15
10
I

16
9

7
17
2
I

18
2

8
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_82683.2_Instance_1 IL_82683.2,IL_7QQX_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_1 IL_82683.27QQX_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_2 IL_82683.2,IL_7QR0_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_2 IL_82683.27QR0_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_3 IL_82683.2,IL_5FQ5_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_3 IL_82683.25FQ5_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_4 IL_82683.2,IL_5B2T_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_4 IL_82683.25B2T_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_5 IL_82683.2,IL_7QQP_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_5 IL_82683.27QQP_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_6 IL_82683.2,IL_7ZO1_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_6 IL_82683.27ZO1_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_7 IL_82683.2,IL_7QR8_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_7 IL_82683.27QR8_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_8 IL_82683.2,IL_5VW1_001,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_8 IL_82683.25VW1_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_9 IL_82683.2,IL_5F9R_001,C58_G29CAAGUUAGAG
IL_82683.2_Sequence_9 IL_82683.25F9R_C58_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_10 IL_82683.2,IL_8KAJ_002,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_10 IL_82683.28KAJ_C40_G29CAAGUU*AGAGtrue100000.00
IL_82683.2_Instance_11 IL_82683.2,IL_8KAL_008,C40_G29CAAGUUAGAG
IL_82683.2_Sequence_11 IL_82683.28KAL_C40_G29CAAGUU*AGAGtrue100000.00

Conserved interactions between motif group positions in IL_82683.2:
1 2 s35 
1 8 cWW 
2 3 s35 
2 8 s55 
3 4 s35 
5 6 cWW 
5 7 s55 
6 7 s35
JAR3D SCFG/MRF model for IL_82683.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000001233745871] | Pair Probability [[0.008763342,0.015714778,0.010074541,0.182671298,0.000000000],[0.018632366,0.008925211,0.291130597,0.012672481,0.000000000],[0.010187681,0.186607373,0.001920315,0.021563540,0.000000000],[0.185039448,0.012209691,0.024600607,0.009286731,0.000000000],[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 [0.004503490,0.990767845,0.004503490,0.000225175] | Right Letter Distribution [0.884615385,0.038461538,0.038461538,0.038461538,0.000000000] | Left Index [1] | Right Index [8] // Basepair C40 - G29 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.884615385,0.038461538,0.038461538,0.038461538,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 7QQX|1|A|G|27
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.884615385,0.038461538,0.038461538,0.038461538,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 7QQX|1|A|A|28
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.038461538,0.884615385,0.038461538,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 7QQX|1|A|G|29
InitialNode  | Left Length Distribution [0.004503490,0.990767845,0.004503490,0.000225175] | Left Letter Distribution [0.038461538,0.038461538,0.038461538,0.884615385,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.038461538,0.884615385,0.038461538,0.000000000] | Position [2] | Left Index [5] | Right Index [7] // Fixed node on right for 7QQX|1|A|A|42
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 [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008301821,0.016122213,0.009106566,0.180403230,0.000000000],[0.020256605,0.009034512,0.181010196,0.010149368,0.000000000],[0.009124327,0.178693612,0.001878500,0.021178825,0.000000000],[0.286949092,0.009533382,0.048973372,0.009284379,0.000000000],[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 U45 - A26 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_82683.2:
> IL_82683.2  7QQX C   40 G   29
CAAGUU*AGAG
> IL_82683.2  7QR0 C   40 G   29
CAAGUU*AGAG
> IL_82683.2  5FQ5 C   40 G   29
CAAGUU*AGAG
> IL_82683.2  5B2T C   40 G   29
CAAGUU*AGAG
> IL_82683.2  7QQP C   40 G   29
CAAGUU*AGAG
> IL_82683.2  7ZO1 C   40 G   29
CAAGUU*AGAG
> IL_82683.2  7QR8 C   40 G   29
CAAGUU*AGAG
> IL_82683.2  5VW1 C   40 G   29
CAAGUU*AGAG
> IL_82683.2  5F9R C   58 G   29
CAAGUU*AGAG
> IL_82683.2  8KAJ C   40 G   29
CAAGUU*AGAG
> IL_82683.2  8KAL C   40 G   29
CAAGUU*AGAG