Alignment of IL_96206.3 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
3
I

6
4


7
3
I

8
2

3
9
2
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_96206.3_Instance_1 IL_96206.3_IL_1S72_017_G554_C605GUAAGC
IL_96206.3_Sequence_1 IL_96206.3_IL_1S72_017_G554_C605GU*AAGCtrue100000.00
IL_96206.3_Instance_2 IL_96206.3_IL_1XJR_004_G19_C31GCGAUC
IL_96206.3_Sequence_2 IL_96206.3_IL_1XJR_004_G19_C31GC*GAUCtrue84001.50

Conserved interactions between motif group positions in IL_96206.3:
1 2 cSS 
1 4 s35 
1 5 cWW 
2 3 cWW 
3 5 cSS 
4 5 s55 
JAR3D SCFG/MRF model for IL_96206.3:
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 [5] // Initial node G554 - C605 from junction 
ClusterNode  | Deletion Probability [0.000000000000015429359482326747000000000000000000000000000000] | Num Left Bases [2] | Num Right Bases [3] | Left Index [1] | Right Index [5] | Norm Constant [0.004696580370998] // Cluster node G554:U555 and A602:C605
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009573432,0.018670696,0.010738592,0.199847452,0.000000000],[0.022636955,0.009050270,0.214230681,0.012151330,0.000000000],[0.010821283,0.200582138,0.002151860,0.023718468,0.000000000],[0.214249849,0.011785171,0.027717608,0.012074217,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U555 - A602 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G554 - C605 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.057311062,0.059127325,0.058376074,0.057761567,0.000000000],[0.062190460,0.060578703,0.008504233,0.053949004,0.000000000],[0.060554353,0.075378184,0.054532050,0.161787815,0.000000000],[0.058781312,0.056539156,0.057004634,0.057624068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G554 - U555 cSS 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.057311062,0.158057807,0.058376074,0.057761567,0.000000000],[0.062190460,0.060578703,0.008504233,0.053949004,0.000000000],[0.060554353,0.075378184,0.054532050,0.062857333,0.000000000],[0.058781312,0.056539156,0.057004634,0.057624068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A602 - C605 cSS 
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A603
Insertion    | Location [4] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion after nucleotide 4, position 4 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 [3] | Right Index [2] // New Initial node after Cluster
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_96206.3:
> IL_96206.3 IL_1S72_017 G  554 C  605
GU*AAGC
> IL_96206.3 IL_1XJR_004 G   19 C   31
GC*GAUC