Alignment of IL_80348.3 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
5

2
5
5
I

6
6


7
5
I

8
5

3
9
4
I

10
3

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_80348.3_Instance_1 IL_80348.3_IL_3U5F_020_U345_A323UGUUUCGA
IL_80348.3_Sequence_1 IL_80348.3_IL_3U5F_020_U345_A323UG*UUUCGAtrue61003.66
IL_80348.3_Instance_2 IL_80348.3_IL_1FJG_012_A274_U252AGUAGU
IL_80348.3_Sequence_2 IL_80348.3_IL_1FJG_012_A274_U252AG*UAGUtrue85001.44
IL_80348.3_Instance_3 IL_80348.3_IL_4IOA_023_U860_A944UGUUA
IL_80348.3_Sequence_3 IL_80348.3_IL_4IOA_023_U860_A944UG*UUAtrue100000.00

Conserved interactions between motif group positions in IL_80348.3:
1 2 perp 
1 5 cWW 
2 3 cWW 
2 4 s55 
3 4 s35 
2 5 6BR
JAR3D SCFG/MRF model for IL_80348.3:
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 U345 - A323 from junction 
BasepairNode | Deletion Probability [0.0000000191968215] | Pair Probability [[0.009072057,0.021359726,0.009720650,0.217473838,0.000000000],[0.022804189,0.009364671,0.191439834,0.010243310,0.000000000],[0.009726197,0.191069331,0.002130991,0.024784794,0.000000000],[0.229856632,0.010219191,0.026177990,0.014556599,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.329462598,0.329462598,0.011072104,0.324331623,0.005401026,0.000270051] | Right Letter Distribution [0.083333333,0.250000000,0.416666667,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair U345 - A323 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Position [2] | Left Index [2] | Right Index [4] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006129019,0.115255522,0.005783824,0.016593279,0.000000000],[0.005376747,0.004290052,0.014193898,0.005732144,0.000000000],[0.028279097,0.082273219,0.006414222,0.670548436,0.000000000],[0.014086021,0.006350540,0.005631856,0.013062123,0.000000000],[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 G346 - U318 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_80348.3:
> IL_80348.3 IL_3U5F_020 U  345 A  323
UG*UUUCGA
> IL_80348.3 IL_1FJG_012 A  274 U  252
AG*UAGU
> IL_80348.3 IL_4IOA_023 U  860 A  944
UG*UUA