Alignment of IL_49976.1 sequences from 3D to the JAR3D model

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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


11
3
I

12
2

5
13
2
I

14
2

6
15
2
I

16
2

7
17
2
I

18
2

8
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_49976.1_Instance_1 IL_49976.1_IL_4BPP_076_G1459_C1490GUAUUUCGUAAUC
IL_49976.1_Sequence_1 IL_49976.1_IL_4BPP_076_G_1459_C_1490GUAUUUC*GUAAUCtrue100000.00

Conserved interactions between motif group positions in IL_49976.1:
1 4 cSS 
1 5 tSS 
1 7 s33 
1 8 cWW 
2 4 s55 
2 5 s53 
2 6 s35 
4 5 cWW 
5 7 cSS 
JAR3D SCFG/MRF model for IL_49976.1:
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 [8] // Initial node G1459 - C1490 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000000001135804345204792700000000000000] | Num Left Bases [4] | Num Right Bases [4] | Left Index [1] | Right Index [8] | Norm Constant [0.001920999614405] // Cluster node G1459:C1465 and G1485:C1490
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.011418641,0.014331648,0.024329846,0.014025501,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.224007246,0.230872701,0.259048862,0.202033724,0.000000000],[0.002491479,0.002491479,0.002491479,0.002491479,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1459 - G1485 tSS 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1465 - G1485 cWW 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1459 - C1490 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.029705719,0.041780930,0.038119887,0.034200529,0.000000000],[0.034799683,0.116975165,0.049301498,0.044283127,0.000000000],[0.040549827,0.390053939,0.020366406,0.039819990,0.000000000],[0.027581711,0.020770301,0.042789515,0.028901774,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1459 - C1465 cSS 
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.072820363,0.068888239,0.070059850,0.070633147,0.000000000],[0.075489748,0.069555755,0.070815126,0.017517776,0.000000000],[0.089448129,0.008485066,0.032344961,0.067217882,0.000000000],[0.072812772,0.070824758,0.070983995,0.072102434,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1485 - A1487 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U1460
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U1462
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U1486
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [3] | Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [7] | Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 7, position 7 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 [5] | Right Index [4] // New Initial node after Cluster
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_49976.1:
> IL_49976.1 IL_4BPP_076 G 1459 C 1490
GUAUUUC*GUAAUC