Alignment of HL_50537.6 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
3

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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HL_50537.6_Instance_1 HL_50537.6,HL_4WJ4_002,A31_U39ACUGUUAAU
HL_50537.6_Sequence_1 HL_50537.64WJ4_A31_U39ACUGUUAAUtrue100000.01
HL_50537.6_Instance_2 HL_50537.6,HL_3KFU_005,G31_C39GCUGUUAAC
HL_50537.6_Sequence_2 HL_50537.63KFU_G31_C39GCUGUUAACtrue100000.00
HL_50537.6_Instance_3 HL_50537.6,HL_1IL2_002,C931_G939CUUGUCGCG
HL_50537.6_Sequence_3 HL_50537.61IL2_C931_G939CUUGUCGCGtrue79002.33
HL_50537.6_Instance_4 HL_50537.6,HL_6MJ0_007,C32_G39CCAGUUAG
HL_50537.6_Sequence_4 HL_50537.66MJ0_C32_G39CCAGUUAGtrue84001.84

Conserved interactions between motif group positions in HL_50537.6:
1 2 s35 
1 5 cWW 
2 5 s55 
4 5 s35
JAR3D SCFG/MRF model for HL_50537.6:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000060823043662] | Pair Probability [[0.009339320,0.018753556,0.010524974,0.206508395,0.000000000],[0.018430728,0.009452306,0.219097689,0.012559761,0.000000000],[0.010550438,0.208651864,0.002037534,0.031117690,0.000000000],[0.195541054,0.012600360,0.024523152,0.010311179,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair A31 - U39 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node C32:A38
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.583333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C32
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U35
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A38
Insertion    | Location [1] | Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.150000000,0.050000000,0.450000000,0.350000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [2] | Length Distribution [0.244498778,0.012224939,0.733649144,0.009168704,0.000458435] | Letter Distribution [0.312500000,0.187500000,0.187500000,0.312500000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_50537.6:
> HL_50537.6  4WJ4 A   31 U   39
ACUGUUAAU
> HL_50537.6  3KFU G   31 C   39
GCUGUUAAC
> HL_50537.6  1IL2 C  931 G  939
CUUGUCGCG
> HL_50537.6  6MJ0 C   32 G   39
CCAGUUAG