Alignment of IL_70237.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_70237.3
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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
3
I

10
4

5
11
5
I

12
6


13
5
I

14
4

6
15
4
I

16
4

7
17
4
I

18
4

8
19
4
I

20
4

9
21
3
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_70237.3_Instance_1 IL_70237.3_IL_1S72_102_U33_A47UACCCGAACA
IL_70237.3_Sequence_1 IL_70237.3_IL_1S72_102_U33_A47UACCC*GAACAtrue92001.04
IL_70237.3_Instance_2 IL_70237.3_IL_3V2F_110_U34_A48UUCCCGAACA
IL_70237.3_Sequence_2 IL_70237.3_IL_3V2F_110_U34_A48UUCCC*GAACAtrue100000.00
IL_70237.3_Instance_3 IL_70237.3_IL_4A1C_007_A32_U45AUCCCGAACU
IL_70237.3_Sequence_3 IL_70237.3_IL_4A1C_007_A32_U45AUCCC*GAACUtrue100000.00
IL_70237.3_Instance_4 IL_70237.3_IL_1MJI_002_A34_U48ACCCCGAACU
IL_70237.3_Sequence_4 IL_70237.3_IL_1MJI_002_A34_U48ACCCC*GAACUtrue97000.39
IL_70237.3_Instance_5 IL_70237.3_IL_3U5H_147_U32_A45UUCCCGAUCA
IL_70237.3_Sequence_5 IL_70237.3_IL_3U5H_147_U32_A45UUCCC*GAUCAtrue89001.53
IL_70237.3_Instance_6 IL_70237.3_IL_2QBG_004_A34_U48ACCCCGAACU
IL_70237.3_Sequence_6 IL_70237.3_IL_2QBG_004_A34_U48ACCCC*GAACUtrue97000.39

Conserved interactions between motif group positions in IL_70237.3:
1 6 s33 
1 10 cWW 
2 3 s35 
4 5 s35 
4 10 cWS 
5 6 cWW 
6 9 tSW 
6 10 s35 
7 8 s35 
8 9 s35 
9 10 s35 
2 1 7BR
8 6 7BR
JAR3D SCFG/MRF model for IL_70237.3:
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 [10] // Initial node U33 - A47 from junction 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [10] | Norm Constant [0.251650942015211] // Cluster node U33:C36 and A47:A47
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.008836923,0.021444779,0.009444062,0.231391450,0.000000000],[0.021450321,0.009062771,0.185760612,0.009937356,0.000000000],[0.009444083,0.185759190,0.002069769,0.024746647,0.000000000],[0.231401709,0.009937264,0.024751992,0.014561070,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U33 - A47 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.011432356,0.021811391,0.011494353,0.016673006,0.000000000],[0.228765464,0.193675299,0.188597845,0.228798602,0.000000000],[0.014037200,0.009841650,0.018209719,0.008628830,0.000000000],[0.013451764,0.014992714,0.009651048,0.009938760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C36 - A47 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.171875000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.328125000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.484375000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.812500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C35
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Cluster
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [1] | Num Right Bases [4] | Left Index [5] | Right Index [9] | Norm Constant [0.257704817211151] // Cluster node C37:C37 and G43:C46
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.009652285,0.016556223,0.011218237,0.185136336,0.000000000],[0.019989741,0.008244143,0.263484907,0.013400077,0.000000000],[0.011361251,0.200559255,0.002068811,0.022890146,0.000000000],[0.186211624,0.012765515,0.026535995,0.009925452,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C37 - G43 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.193309940,0.027745336,0.002379316,0.076728268,0.000000000],[0.055696564,0.025093188,0.025457850,0.017196014,0.000000000],[0.064841819,0.294535384,0.002379316,0.010117074,0.000000000],[0.022532745,0.014381501,0.157640183,0.009965502,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G43 - C46 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A44
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.796875000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.171875000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A45
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 [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_70237.3:
> IL_70237.3 IL_1S72_102 U   33 A   47
UACCC*GAACA
> IL_70237.3 IL_3V2F_110 U   34 A   48
UUCCC*GAACA
> IL_70237.3 IL_4A1C_007 A   32 U   45
AUCCC*GAACU
> IL_70237.3 IL_1MJI_002 A   34 U   48
ACCCC*GAACU
> IL_70237.3 IL_3U5H_147 U   32 A   45
UUCCC*GAUCA
> IL_70237.3 IL_2QBG_004 A   34 U   48
ACCCC*GAACU