Alignment of HL_13963.3 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
3

2
5
3
I

6
3

3
7
2
I

8
2

4
9
1
I


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HL_13963.3_Instance_1 HL_13963.3,HL_361D_002,G86_C90GGCGAC
HL_13963.3_Sequence_1 HL_13963.3361D_G86_C90GGCGACtrue100000.00
HL_13963.3_Instance_2 HL_13963.3,HL_361D_001,G86_C90GGCGAC
HL_13963.3_Sequence_2 HL_13963.3361D_G86_C90GGCGACtrue100000.00
HL_13963.3_Instance_3 HL_13963.3,HL_2ZZM_002,G31_C39GCCUAGGAC
HL_13963.3_Sequence_3 HL_13963.32ZZM_G31_C39GCCUAGGACtrue43005.45
HL_13963.3_Instance_4 HL_13963.3,HL_5J7L_163,G1171_C1178GCUUAUGC
HL_13963.3_Sequence_4 HL_13963.35J7L_G_1171_C_1178GCUUAUGCtrue39005.77

Conserved interactions between motif group positions in HL_13963.3:
1 2 s35 
1 4 cWW 
3 4 s35
JAR3D SCFG/MRF model for HL_13963.3:
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 [0.0000060823043662] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair G86 - C90 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G87:A89A
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[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 G87
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A89A
Insertion    | Location [1] | Length Distribution [0.000000000,0.006093845,0.490554540,0.249847654,0.006398537,0.243906155,0.003046923,0.000152346] | Letter Distribution [0.178571429,0.250000000,0.321428571,0.250000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_13963.3:
> HL_13963.3  361D G   86 C   90
GGCGAC
> HL_13963.3  361D G   86 C   90
GGCGAC
> HL_13963.3  2ZZM G   31 C   39
GCCUAGGAC
> HL_13963.3  5J7L G 1171 C 1178
GCUUAUGC