Alignment of IL_87065.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_87065.1
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
3
I

4
4

2
5
4
I

6
5


7
4
I

8
4

3
9
3
I

10
2

4
11
2
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_87065.1_Instance_1 IL_87065.1_IL_4A1B_094_G2391_C2972GAAUACC
IL_87065.1_Sequence_1 IL_87065.1_IL_4A1B_094_G_2391_C_2972GAA*UACCtrue100000.00
IL_87065.1_Instance_2 IL_87065.1_IL_3U5H_097_G2396_C2984GAAUACC
IL_87065.1_Sequence_2 IL_87065.1_IL_3U5H_097_G_2396_C_2984GAA*UACCtrue100000.00
IL_87065.1_Instance_3 IL_87065.1_IL_2QBG_079_A2054_U2615ACGCUAU
IL_87065.1_Sequence_3 IL_87065.1_IL_2QBG_079_A_2054_U_2615ACG*CUAUtrue68003.04

Conserved interactions between motif group positions in IL_87065.1:
1 5 cWW 
2 3 cWW 
4 5 cSH 
5 4 7BR
JAR3D SCFG/MRF model for IL_87065.1:
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 [5] // Initial node G2391 - C2972 from junction 
ClusterNode  | Deletion Probability [0.0000000034550030] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [5] | Norm Constant [0.305651423960523] // Cluster node G2391:G2391 and A2970:C2972
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.004733746,0.037240585,0.005339211,0.240859165,0.000000000],[0.008690836,0.014981024,0.097250365,0.012347507,0.000000000],[0.005288794,0.395468482,0.001029139,0.030717388,0.000000000],[0.094380619,0.024015626,0.011358393,0.016299118,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2391 - C2972 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.101253721,0.135894093,0.006054057,0.060998411,0.000000000],[0.104207646,0.097420758,0.001164766,0.100868758,0.000000000],[0.005756469,0.006285621,0.013783047,0.100415395,0.000000000],[0.058267301,0.110073967,0.001164766,0.096391223,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2970 - C2972 cSH 
Insertion    | Location [2] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009472747,0.022988174,0.010372983,0.225098889,0.000000000],[0.018936855,0.008916940,0.195696316,0.011163054,0.000000000],[0.010312898,0.208310389,0.002127705,0.027444663,0.000000000],[0.199992661,0.011428674,0.023422512,0.014314540,0.000000000],[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 [2] | Right Index [3] // Basepair A2393 - U2969 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_87065.1:
> IL_87065.1 IL_4A1B_094 G 2391 C 2972
GAA*UACC
> IL_87065.1 IL_3U5H_097 G 2396 C 2984
GAA*UACC
> IL_87065.1 IL_2QBG_079 A 2054 U 2615
ACG*CUAU