Alignment of IL_99646.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_99646.2
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


11
5
I

12
5

5
13
4
I

14
4

6
15
3
I

16
3

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_99646.2_Instance_1 IL_99646.2,IL_5J7L_297,C1437_G1555CUAUAAAUG
IL_99646.2_Sequence_1 IL_99646.25J7L_C_1437_G_1555CUAU*AAAUGtrue97000.33
IL_99646.2_Instance_2 IL_99646.2,IL_7A0S_053,C1451_G1571CUAUAAACG
IL_99646.2_Sequence_2 IL_99646.27A0S_C_1451_G_1571CUAU*AAACGtrue92000.84
IL_99646.2_Instance_3 IL_99646.2,IL_9DFE_056,C1437_G1555CUAGCGAAG
IL_99646.2_Sequence_3 IL_99646.29DFE_C_1437_G_1555CUAG*CGAAGtrue100000.00
IL_99646.2_Instance_4 IL_99646.2,IL_2ZY6_001,A7_U29AUAGCGAGU
IL_99646.2_Sequence_4 IL_99646.22ZY6_A7_U29AUAG*CGAGUtrue94000.61
IL_99646.2_Instance_5 IL_99646.2,IL_9DFE_009,A357_U284AUAGCGAAU
IL_99646.2_Sequence_5 IL_99646.29DFE_A357_U284AUAG*CGAAUtrue99000.10
IL_99646.2_Instance_6 IL_99646.2,IL_4WF9_054,C1624_G1465CUAGCGAUG
IL_99646.2_Sequence_6 IL_99646.24WF9_C_1624_G_1465CUAG*CGAUGtrue100000.00

Conserved interactions between motif group positions in IL_99646.2:
1 2 s35 
1 8 cWW 
2 3 s35 
2 6 s33 
2 7 tWH 
2 8 s55 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
3 6 6BR
JAR3D SCFG/MRF model for IL_99646.2:
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 [0.0000001231336240] | Pair Probability [[0.009095347,0.018030680,0.010213250,0.211864073,0.000000000],[0.018626536,0.009303721,0.234075226,0.012169473,0.000000000],[0.010286044,0.193360117,0.001995306,0.032122363,0.000000000],[0.192053984,0.012061081,0.024555413,0.010187385,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.312500000,0.187500000,0.187500000,0.312500000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C1437 - G1555 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017712837,0.003919879,0.018397680,0.003919879,0.000000000],[0.039419550,0.315867349,0.003919879,0.003919879,0.000000000],[0.003919879,0.009396209,0.029810350,0.017434273,0.000000000],[0.467089651,0.003919879,0.022742669,0.038610158,0.000000000],[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 [7] // Basepair U1438 - A1553 tWH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.149445559,0.129024331,0.188456150,0.131352616,0.000000000],[0.075351379,0.093920228,0.001433690,0.127027567,0.000000000],[0.001433690,0.001433690,0.009544417,0.001433690,0.000000000],[0.007681561,0.001433690,0.079594054,0.001433690,0.000000000],[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 [3] | Right Index [6] // Basepair A1439 - A1552 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009142061,0.018632113,0.010289247,0.192120101,0.000000000],[0.018038906,0.009276676,0.193426307,0.012064516,0.000000000],[0.010216480,0.234139331,0.001995996,0.024562720,0.000000000],[0.211934506,0.012172508,0.032144854,0.009843678,0.000000000],[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 [4] | Right Index [5] // Basepair U1440 - A1551 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_99646.2:
> IL_99646.2  5J7L C 1437 G 1555
CUAU*AAAUG
> IL_99646.2  7A0S C 1451 G 1571
CUAU*AAACG
> IL_99646.2  9DFE C 1437 G 1555
CUAG*CGAAG
> IL_99646.2  2ZY6 A    7 U   29
AUAG*CGAGU
> IL_99646.2  9DFE A  357 U  284
AUAG*CGAAU
> IL_99646.2  4WF9 C 1624 G 1465
CUAG*CGAUG