Alignment of IL_54966.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_54966.1
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
6
I

10
7


11
6
I

12
6

5
13
5
I

14
4

6
15
4
I

16
4

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_54966.1_Instance_1 IL_54966.1_IL_1FJG_055_G1401_C1501GCCCGUAAC
IL_54966.1_Sequence_1 IL_54966.1_IL_1FJG_055_G_1401_C_1501GCCC*GUAACtrue100000.00
IL_54966.1_Instance_2 IL_54966.1_IL_2AW7_061_G1401_C1501GCCCGUAAC
IL_54966.1_Sequence_2 IL_54966.1_IL_2AW7_061_G_1401_C_1501GCCC*GUAACtrue100000.00
IL_54966.1_Instance_3 IL_54966.1_IL_3U5F_081_G1638_C1764GCCCGUAAC
IL_54966.1_Sequence_3 IL_54966.1_IL_3U5F_081_G_1638_C_1764GCCC*GUAACtrue100000.00
IL_54966.1_Instance_4 IL_54966.1_IL_4BPP_081_G1610_C1717GCCCGUAAC
IL_54966.1_Sequence_4 IL_54966.1_IL_4BPP_081_G_1610_C_1717GCCC*GUAACtrue100000.00

Conserved interactions between motif group positions in IL_54966.1:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 cWW 
3 4 s35 
3 7 cSW 
4 5 cWW 
4 7 s55 
5 6 s35 
6 7 cSH 
7 8 s35 
8 9 s35 
JAR3D SCFG/MRF model for IL_54966.1:
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 [9] // Initial node G1401 - C1501 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009999033,0.020370037,0.011577394,0.189754219,0.000000000],[0.016871198,0.008244913,0.204374808,0.013008374,0.000000000],[0.011431659,0.249278495,0.002108170,0.027040831,0.000000000],[0.188658474,0.013655008,0.023325621,0.010301767,0.000000000],[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 [9] // Basepair G1401 - C1501 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.011872772,0.014708582,0.014301144,0.033757857,0.000000000],[0.399542582,0.017945751,0.034889197,0.016036878,0.000000000],[0.014645019,0.028896488,0.003610810,0.015133880,0.000000000],[0.041074697,0.014455142,0.324408656,0.014720545,0.000000000],[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 [8] // Basepair C1402 - A1500 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [7] | Norm Constant [0.326407563543262] // Cluster node C1403:C1403 and U1498:A1499
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.177419266,0.022538031,0.009786791,0.007644646,0.000000000],[0.238046717,0.018024818,0.009854628,0.008394557,0.000000000],[0.172050331,0.019796743,0.093017756,0.006569858,0.000000000],[0.180923828,0.019886693,0.009052772,0.006992564,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1403 - A1499 cSW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.021745117,0.127570845,0.025990805,0.016040998,0.000000000],[0.031117562,0.014978621,0.002550147,0.017709157,0.000000000],[0.011100813,0.205739968,0.053341346,0.018363188,0.000000000],[0.293476277,0.144133058,0.002550147,0.013591951,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1498 - A1499 cSH 
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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[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 C1404 - G1497 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_54966.1:
> IL_54966.1 IL_1FJG_055 G 1401 C 1501
GCCC*GUAAC
> IL_54966.1 IL_2AW7_061 G 1401 C 1501
GCCC*GUAAC
> IL_54966.1 IL_3U5F_081 G 1638 C 1764
GCCC*GUAAC
> IL_54966.1 IL_4BPP_081 G 1610 C 1717
GCCC*GUAAC