Alignment of IL_83389.2 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
3

2
5
3
I

6
4


7
3
I

8
3

3
9
2
I

10
2

4
11
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_83389.2_Instance_1 IL_83389.2,IL_4V9F_073,A2095_U2650AAGCUAU
IL_83389.2_Sequence_1 IL_83389.24V9F_A_2095_U_2650AAG*CUAUtrue100000.00
IL_83389.2_Instance_2 IL_83389.2,IL_4WF9_079,A2081_U2642ACGCUAU
IL_83389.2_Sequence_2 IL_83389.24WF9_A_2081_U_2642ACG*CUAUtrue96000.34
IL_83389.2_Instance_3 IL_83389.2,IL_5J7L_321,A2054_U2615ACGCUAU
IL_83389.2_Sequence_3 IL_83389.25J7L_A_2054_U_2615ACG*CUAUtrue96000.34
IL_83389.2_Instance_4 IL_83389.2,IL_8P9A_320,G2396_C2984GAAUACC
IL_83389.2_Sequence_4 IL_83389.28P9A_G_2396_C_2984GAA*UACCtrue95000.44
IL_83389.2_Instance_5 IL_83389.2,IL_8CRE_097,G2374_C2956GAAUACC
IL_83389.2_Sequence_5 IL_83389.28CRE_G_2374_C_2956GAA*UACCtrue95000.44

Conserved interactions between motif group positions in IL_83389.2:
1 4 cWW 
2 3 cWW
JAR3D SCFG/MRF model for IL_83389.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [4] // Initial node
BasepairNode | Deletion Probability [0.0000000000030927] | Pair Probability [[0.009192854,0.020706043,0.010085615,0.225768905,0.000000000],[0.016854189,0.009292783,0.192061375,0.011199507,0.000000000],[0.010026535,0.214869253,0.002001534,0.041416213,0.000000000],[0.191480098,0.011785275,0.022529294,0.010730527,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.500000000,0.357142857,0.071428571,0.071428571,0.000000000] | Right Length Distribution [0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.458333333,0.208333333,0.041666667,0.291666667,0.000000000] | Left Index [1] | Right Index [4] // Basepair A2095 - U2650 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009280432,0.020368229,0.010312873,0.215702181,0.000000000],[0.016772457,0.009285906,0.193782875,0.011767824,0.000000000],[0.010233627,0.226772067,0.002010885,0.036277626,0.000000000],[0.192008674,0.012321377,0.022616385,0.010486579,0.000000000],[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 G2097 - C2647 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_83389.2:
> IL_83389.2  4V9F A 2095 U 2650
AAG*CUAU
> IL_83389.2  4WF9 A 2081 U 2642
ACG*CUAU
> IL_83389.2  5J7L A 2054 U 2615
ACG*CUAU
> IL_83389.2  8P9A G 2396 C 2984
GAA*UACC
> IL_83389.2  8CRE G 2374 C 2956
GAA*UACC