Alignment of IL_90133.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_90133.3
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
4
I

6
7

3
7
8
I

8
9


9
8
I

10
7

4
11
7
I

12
7

5
13
6
I

14
5

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_90133.3_Instance_1 IL_90133.3_IL_3U5F_028_G516_C536GUAUAAC
IL_90133.3_Sequence_1 IL_90133.3_IL_3U5F_028_G516_C536GUA*UAACtrue80001.93
IL_90133.3_Instance_2 IL_90133.3_IL_3V2F_031_G875_C902GCUAAAC
IL_90133.3_Sequence_2 IL_90133.3_IL_3V2F_031_G875_C902GCU*AAACtrue84001.52
IL_90133.3_Instance_3 IL_90133.3_IL_2AW7_006_C67_G102CGGCGAG
IL_90133.3_Sequence_3 IL_90133.3_IL_2AW7_006_C67_G102CGG*CGAGtrue100000.00
IL_90133.3_Instance_4 IL_90133.3_IL_1S72_053_A1465_U1478ACCGACU
IL_90133.3_Sequence_4 IL_90133.3_IL_1S72_053_A_1465_U_1478ACC*GACUtrue77002.17
IL_90133.3_Instance_5 IL_90133.3_IL_3U5F_068_U1276_A1436UGGUCUGUGA
IL_90133.3_Sequence_5 IL_90133.3_IL_3U5F_068_U_1276_A_1436UGG*UCUGUGAtrue59003.93
IL_90133.3_Instance_6 IL_90133.3_IL_4BPP_066_U1248_A1407UGGUCUGUGA
IL_90133.3_Sequence_6 IL_90133.3_IL_4BPP_066_U_1248_A_1407UGG*UCUGUGAtrue59003.93

Conserved interactions between motif group positions in IL_90133.3:
1 2 s35 
1 7 cWW 
2 3 s35 
2 7 s55 
3 4 cWW 
3 5 tSH 
5 6 s35 
6 7 s35 
JAR3D SCFG/MRF model for IL_90133.3:
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 [7] // Initial node G516 - C536 from junction 
BasepairNode | Deletion Probability [0.0000040507541457] | Pair Probability [[0.009286488,0.019798872,0.010378792,0.203290480,0.000000000],[0.019928641,0.008620290,0.203764573,0.011464360,0.000000000],[0.010357661,0.214071747,0.002069606,0.024700235,0.000000000],[0.213844488,0.011558359,0.024769722,0.012095683,0.000000000],[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 [0.661815186,0.335026775,0.003020733,0.000137306] | Right Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G516 - C536 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.312500000,0.437500000,0.187500000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000034668202] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [5] | Norm Constant [0.271490520016192] // Cluster node A518:A518 and U533:A534
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.011482008,0.112765157,0.011905390,0.153344322,0.000000000],[0.017883524,0.009447760,0.151510989,0.012622831,0.000000000],[0.011794866,0.153462523,0.002487231,0.146131042,0.000000000],[0.151182686,0.013156782,0.021350858,0.019472030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A518 - U533 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.083316030,0.057750357,0.002817434,0.213979904,0.000000000],[0.097281044,0.044047618,0.002817434,0.002817434,0.000000000],[0.059598005,0.002817434,0.257800837,0.030806940,0.000000000],[0.076365633,0.062149028,0.002817434,0.002817434,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A518 - A534 tSH 
Insertion    | Location [2] | Length Distribution [0.659069065,0.008238363,0.329809145,0.002746121,0.000137306] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
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 [4] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_90133.3:
> IL_90133.3 IL_3U5F_028 G  516 C  536
GUA*UAAC
> IL_90133.3 IL_3V2F_031 G  875 C  902
GCU*AAAC
> IL_90133.3 IL_2AW7_006 C   67 G  102
CGG*CGAG
> IL_90133.3 IL_1S72_053 A 1465 U 1478
ACC*GACU
> IL_90133.3 IL_3U5F_068 U 1276 A 1436
UGG*UCUGUGA
> IL_90133.3 IL_4BPP_066 U 1248 A 1407
UGG*UCUGUGA