Alignment of IL_82188.2 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
3
I

6
4

3
7
5
I

8
6

4
9
7
I

10
8

5
11
9
I

12
10

6
13
11
I

14
20

7
15
20
I

16
21


17
20
I

18
20

8
19
19
I

20
18

9
21
17
I

22
16

10
23
15
I

24
14

11
25
13
I

26
12

12
27
3
I

28
3

13
29
2
I

30
2

14
31
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_82188.2_Instance_1 IL_82188.2_IL_4A1B_090_U2206_G2229UCAAAGUAACCAAG
IL_82188.2_Sequence_1 IL_82188.2_IL_4A1B_090_U_2206_G_2229UCAAAGU*AACCAAGtrue99000.10
IL_82188.2_Instance_2 IL_82188.2_IL_1S72_069_U1907_G1932UGAACACGACGAAG
IL_82188.2_Sequence_2 IL_82188.2_IL_1S72_069_U_1907_G_1932UGAACAC*GACGAAGtrue100000.00
IL_82188.2_Instance_3 IL_82188.2_IL_2QBZ_005_A60_U81AAAAAUGCGCCAAU
IL_82188.2_Sequence_3 IL_82188.2_IL_2QBZ_005_A60_U81AAAAAUG*CGCCAAUtrue94000.99
IL_82188.2_Instance_4 IL_82188.2_IL_2OIU_002_C21_G40CGACCAGCUCUUAG
IL_82188.2_Sequence_4 IL_82188.2_IL_2OIU_002_C21_G40CGACCAG*CUCUUAGtrue85002.60

Conserved interactions between motif group positions in IL_82188.2:
1 2 s35 
1 14 cWW 
2 11 s33 
2 13 tSH 
3 4 s35 
3 12 s55 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s35 
10 11 s35 
12 13 s35 
13 14 s35 
13 2 6BR
JAR3D SCFG/MRF model for IL_82188.2:
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 [14] // Initial node U2206 - G2229 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.011111603,0.017461516,0.012891603,0.128456516,0.000000000],[0.165459031,0.012258289,0.131655760,0.014499055,0.000000000],[0.013096582,0.117654275,0.002783975,0.020240771,0.000000000],[0.120520778,0.013521174,0.204788661,0.013600411,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair U2206 - G2229 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.139603202,0.125397335,0.001423599,0.008606663,0.000000000],[0.140035475,0.099564092,0.001423599,0.001423599,0.000000000],[0.148901219,0.001423599,0.009176075,0.064154364,0.000000000],[0.130375178,0.125644805,0.001423599,0.001423599,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair C2207 - A2228 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.250000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [5] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.416666667,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [12] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [6] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Position [1] | Left Index [6] | Right Index [12] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [7] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.083333333,0.250000000,0.000000000] | Position [2] | Left Index [7] | Right Index [12] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.250000000,0.250000000,0.000000000] | Position [2] | Left Index [7] | Right Index [11] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [7] | 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Position [2] | Left Index [7] | Right Index [9] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009694180,0.019340841,0.011054737,0.192879225,0.000000000],[0.019536413,0.008560570,0.212050526,0.012463012,0.000000000],[0.011022420,0.223001642,0.002109324,0.025151587,0.000000000],[0.204201759,0.012606770,0.025255099,0.011071894,0.000000000],[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 [7] | Right Index [8] // Basepair U2212 - A2223 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_82188.2:
> IL_82188.2 IL_4A1B_090 U 2206 G 2229
UCAAAGU*AACCAAG
> IL_82188.2 IL_1S72_069 U 1907 G 1932
UGAACAC*GACGAAG
> IL_82188.2 IL_2QBZ_005 A   60 U   81
AAAAAUG*CGCCAAU
> IL_82188.2 IL_2OIU_002 C   21 G   40
CGACCAG*CUCUUAG