Alignment of IL_08926.3 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
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_08926.3_Instance_1 IL_08926.3_IL_3V2F_093_C2507_G2582CGUGG
IL_08926.3_Sequence_1 IL_08926.3_IL_3V2F_093_C_2507_G_2582CG*UGGtrue100000.00
IL_08926.3_Instance_2 IL_08926.3_IL_3U5H_113_C2876_G2951CGUGG
IL_08926.3_Sequence_2 IL_08926.3_IL_3U5H_113_C_2876_G_2951CG*UGGtrue100000.00
IL_08926.3_Instance_3 IL_08926.3_IL_1S72_084_C2542_G2617CGUGG
IL_08926.3_Sequence_3 IL_08926.3_IL_1S72_084_C_2542_G_2617CG*UGGtrue100000.00
IL_08926.3_Instance_4 IL_08926.3_IL_1S72_081_U2528_G2494UGUCG
IL_08926.3_Sequence_4 IL_08926.3_IL_1S72_081_U_2528_G_2494UG*UCGtrue93000.74
IL_08926.3_Instance_5 IL_08926.3_IL_3U5H_110_U2862_G2828UGUUG
IL_08926.3_Sequence_5 IL_08926.3_IL_3U5H_110_U_2862_G_2828UG*UUGtrue78002.47
IL_08926.3_Instance_6 IL_08926.3_IL_4BPP_018_U336_A314UGUCUCGA
IL_08926.3_Sequence_6 IL_08926.3_IL_4BPP_018_U336_A314UG*UCUCGAtrue31007.67

Conserved interactions between motif group positions in IL_08926.3:
1 2 s35 
1 5 cWW 
2 3 cWW 
2 5 s55 
3 4 s33 
4 5 cHH 
JAR3D SCFG/MRF model for IL_08926.3:
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 C2507 - G2582 from junction 
ClusterNode  | Deletion Probability [0.0000000083323644] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [5] | Norm Constant [0.287606645399910] // Cluster node C2507:C2507 and G2581:G2582
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.010463773,0.016250536,0.012173131,0.138240069,0.000000000],[0.115596488,0.010802910,0.177348529,0.013966399,0.000000000],[0.012360245,0.143711858,0.002511480,0.020205985,0.000000000],[0.151719213,0.013091915,0.149769567,0.011787900,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2507 - G2582 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.005352624,0.005352624,0.005352624,0.005352624,0.000000000],[0.037248401,0.005352624,0.208153515,0.005352624,0.000000000],[0.005352624,0.288273431,0.370197384,0.005352624,0.000000000],[0.005352624,0.005352624,0.037248401,0.005352624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2581 - G2582 cHH 
Insertion    | Location [2] | Length Distribution [0.824969064,0.006874742,0.001718686,0.164993813,0.001374948,0.000068747] | Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
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 [2] | Right Index [3] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015877772,0.298579733,0.014983514,0.042986372,0.000000000],[0.013928943,0.011113763,0.036770561,0.014849632,0.000000000],[0.014651906,0.042627226,0.003323323,0.388936094,0.000000000],[0.036491097,0.016451640,0.014589827,0.033838598,0.000000000],[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 G2508 - U2580 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_08926.3:
> IL_08926.3 IL_3V2F_093 C 2507 G 2582
CG*UGG
> IL_08926.3 IL_3U5H_113 C 2876 G 2951
CG*UGG
> IL_08926.3 IL_1S72_084 C 2542 G 2617
CG*UGG
> IL_08926.3 IL_1S72_081 U 2528 G 2494
UG*UCG
> IL_08926.3 IL_3U5H_110 U 2862 G 2828
UG*UUG
> IL_08926.3 IL_4BPP_018 U  336 A  314
UG*UCUCGA