Alignment of IL_80494.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_80494.2
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
5
I

8
8

4
9
8
I

10
9

5
11
9
I

12
10

6
13
10
I

14
11


15
10
I

16
10

7
17
9
I

18
9

8
19
8
I

20
8

9
21
7
I

22
6

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_80494.2_Instance_1 IL_80494.2_IL_3P49_012_G116_C138GCAAAGCCUAAAC
IL_80494.2_Sequence_1 IL_80494.2_IL_3P49_012_G116_C138GCAAAG*CCUAAACtrue97000.58
IL_80494.2_Instance_2 IL_80494.2_IL_1S72_057_C1578_G1618CCAACUACGAACG
IL_80494.2_Sequence_2 IL_80494.2_IL_1S72_057_C_1578_G_1618CCAACU*ACGAACGtrue100000.00
IL_80494.2_Instance_3 IL_80494.2_IL_3B5F_001_C4_G11CAGUCCGAGAAG
IL_80494.2_Sequence_3 IL_80494.2_IL_3B5F_001_C4_G11CAGUCC*GAGAAGtrue83003.08

Conserved interactions between motif group positions in IL_80494.2:
1 2 s35 
1 12 cWW 
2 11 tWH 
3 4 s35 
3 10 s55 
4 5 s35 
4 9 tHS 
5 6 s35 
5 8 bif 
6 7 cWW 
7 8 s35 
8 9 s35 
10 11 s35 
11 12 s35 
9 3 6BPh
JAR3D SCFG/MRF model for IL_80494.2:
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 [12] // Initial node G116 - C138 from junction 
BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.009987650,0.018214897,0.011593253,0.190884602,0.000000000],[0.019392976,0.008431163,0.230141683,0.013571804,0.000000000],[0.011642323,0.218263837,0.002128924,0.024805687,0.000000000],[0.191253546,0.013354078,0.026056620,0.010276957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G116 - C138 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.074666681,0.002371906,0.132889684,0.002371906,0.000000000],[0.256608086,0.011223810,0.219910394,0.002371906,0.000000000],[0.002371906,0.002371906,0.016201685,0.024496808,0.000000000],[0.023560072,0.002371906,0.011353789,0.214857553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair C117 - A136 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.033030289,0.033218255,0.270737673,0.156541726,0.000000000],[0.049633289,0.032263812,0.002877357,0.129470953,0.000000000],[0.000559599,0.000559599,0.016727646,0.001599435,0.000000000],[0.002956685,0.000559599,0.267664647,0.001599435,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A119 - U134 tHS 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.019151570,0.404305861,0.005214221,0.005214221,0.000000000],[0.076986253,0.405940340,0.005214221,0.005214221,0.000000000],[0.005214221,0.005214221,0.018305611,0.005214221,0.000000000],[0.005214221,0.005214221,0.023168158,0.005214221,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A120 - C133 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009685694,0.019182219,0.010986155,0.195803621,0.000000000],[0.020623118,0.008749922,0.213456437,0.012400460,0.000000000],[0.010991697,0.213086471,0.002130191,0.024759915,0.000000000],[0.208179451,0.012376361,0.026149698,0.011438589,0.000000000],[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 G121 - C132 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_80494.2:
> IL_80494.2 IL_3P49_012 G  116 C  138
GCAAAG*CCUAAAC
> IL_80494.2 IL_1S72_057 C 1578 G 1618
CCAACU*ACGAACG
> IL_80494.2 IL_3B5F_001 C    4 G   11
CAGUCC*GAGAAG