Alignment of IL_85536.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_85536.2
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

6
13
7
I

14
8


15
7
I

16
7

7
17
6
I

18
6

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_85536.2_Instance_1 IL_85536.2,IL_8CRE_465,G1527_C1558GGGAUAUUCAAC
IL_85536.2_Sequence_1 IL_85536.28CRE_G_1527_C_1558GGGAUA*UUCAACtrue98000.27
IL_85536.2_Instance_2 IL_85536.2,IL_8P9A_451,G1540_C1571GGGAUAUUCAAC
IL_85536.2_Sequence_2 IL_85536.28P9A_G_1540_C_1571GGGAUA*UUCAACtrue98000.27
IL_85536.2_Instance_3 IL_85536.2,IL_4LFB_055,C1303_G1334CGGAUUAUGAAG
IL_85536.2_Sequence_3 IL_85536.24LFB_C_1303_G_1334CGGAUU*AUGAAGtrue100000.00
IL_85536.2_Instance_4 IL_85536.2,IL_5J7L_057,C1303_G1334CGGAUUAUGAAG
IL_85536.2_Sequence_4 IL_85536.25J7L_C_1303_G_1334CGGAUU*AUGAAGtrue100000.00
IL_85536.2_Instance_5 IL_85536.2,IL_8P9A_254,C768_G763CGGAUGCUGAUG
IL_85536.2_Sequence_5 IL_85536.28P9A_C768_G763CGGAUG*CUGAUGtrue99000.11
IL_85536.2_Instance_6 IL_85536.2,IL_8CRE_028,C764_G759CGGAUGCUGAUG
IL_85536.2_Sequence_6 IL_85536.28CRE_C764_G759CGGAUG*CUGAUGtrue99000.11
IL_85536.2_Instance_7 IL_85536.2,IL_8P9A_410,G703_C735GCUAACGCGAAC
IL_85536.2_Sequence_7 IL_85536.28P9A_G703_C735GCUAAC*GCGAACtrue86002.33
IL_85536.2_Instance_8 IL_85536.2,IL_6AAY_001,U49_G32UAAUCACGGAACUG
IL_85536.2_Sequence_8 IL_85536.26AAY_U49_G32UAAUCAC*GGAACUGtrue280011.68

Conserved interactions between motif group positions in IL_85536.2:
1 2 s35 
1 12 cWW 
2 3 s35 
2 11 tSH 
2 12 s55 
3 4 s35 
3 9 s33 
3 10 tSH 
4 5 s35 
4 9 tHS 
4 10 s55 
5 6 s35 
5 8 cWW 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
10 11 s35 
11 12 s35 
3 9 6BR
JAR3D SCFG/MRF model for IL_85536.2:
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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009278404,0.016906130,0.010788355,0.169574323,0.000000000],[0.051346638,0.011266779,0.212625296,0.013109916,0.000000000],[0.010839801,0.202051421,0.002117091,0.022292708,0.000000000],[0.175653840,0.012890456,0.069241210,0.010017632,0.000000000],[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 [12] // Basepair G1527 - C1558 cWW 
BasepairNode | Deletion Probability [0.0000123078457223] | Pair Probability [[0.084933715,0.093222472,0.001568551,0.032594848,0.000000000],[0.102819504,0.081818001,0.001568551,0.001568551,0.000000000],[0.182641940,0.001568551,0.009361557,0.162901424,0.000000000],[0.138440989,0.101854243,0.001568551,0.001568551,0.000000000],[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 [0.869396619,0.129517605,0.001046999,0.000038778] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1528 - A1557 tSH 
BasepairNode | Deletion Probability [0.0000123078457223] | Pair Probability [[0.085957335,0.062700582,0.000710990,0.003350898,0.000000000],[0.059667795,0.062555393,0.000710990,0.000710990,0.000000000],[0.332049366,0.002590235,0.012662837,0.219849361,0.000000000],[0.092843574,0.062217676,0.000710990,0.000710990,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair G1529 - A1556 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.118911887,0.139363241,0.174330587,0.124654734,0.000000000],[0.107371957,0.110896088,0.001353176,0.120174574,0.000000000],[0.001353176,0.001353176,0.007544025,0.001353176,0.000000000],[0.006495508,0.001353176,0.082138342,0.001353176,0.000000000],[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 [4] | Right Index [9] // Basepair A1530 - C1555 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.016075941,0.246526312,0.062907297,0.022889954,0.000000000],[0.015190268,0.015539385,0.019667265,0.017132350,0.000000000],[0.051744375,0.020498092,0.003787742,0.072482833,0.000000000],[0.019958610,0.018442326,0.015665473,0.381491779,0.000000000],[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 [5] | Right Index [8] // Basepair U1531 - U1554 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008874834,0.018163668,0.009886445,0.207536427,0.000000000],[0.018165448,0.009130305,0.208151098,0.011446284,0.000000000],[0.009886458,0.208149880,0.001951325,0.029866332,0.000000000],[0.207539466,0.011446018,0.029877333,0.009928679,0.000000000],[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 [6] | Right Index [7] // Basepair A1532 - U1553 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_85536.2:
> IL_85536.2  8CRE G 1527 C 1558
GGGAUA*UUCAAC
> IL_85536.2  8P9A G 1540 C 1571
GGGAUA*UUCAAC
> IL_85536.2  4LFB C 1303 G 1334
CGGAUU*AUGAAG
> IL_85536.2  5J7L C 1303 G 1334
CGGAUU*AUGAAG
> IL_85536.2  8P9A C  768 G  763
CGGAUG*CUGAUG
> IL_85536.2  8CRE C  764 G  759
CGGAUG*CUGAUG
> IL_85536.2  8P9A G  703 C  735
GCUAAC*GCGAAC
> IL_85536.2  6AAY U   49 G   32
UAAUCAC*GGAACUG