Alignment of HL_25061.1 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_25061.1_Instance_1 HL_25061.1,HL_6MWN_003,U624_G632UGUGAGAGG
HL_25061.1_Sequence_1 HL_25061.16MWN_U624_G632UGUGAGAGGtrue100000.00
HL_25061.1_Instance_2 HL_25061.1,HL_8CRE_028,C1343_G1353CUGUUUUGACG
HL_25061.1_Sequence_2 HL_25061.18CRE_C_1343_G_1353CUGUUUUGACGtrue84002.12

Conserved interactions between motif group positions in HL_25061.1:
1 4 s35 
1 5 cWW 
2 3 perp 
2 4 s53 
3 4 perp 
4 5 s55
JAR3D SCFG/MRF model for HL_25061.1:
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 [0.0000001182498160] | Pair Probability [[0.010391363,0.015542673,0.012620534,0.118031974,0.000000000],[0.161407275,0.018831736,0.135468706,0.014912387,0.000000000],[0.012838381,0.120099009,0.002697951,0.019069108,0.000000000],[0.143779637,0.013983083,0.188496931,0.011829251,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.375000000,0.375000000,0.125000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair U624 - G632 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G625:A630
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G625
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U626
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A630
Insertion    | Location [1] | Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [2] | Length Distribution [0.000000000,0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.187500000,0.062500000,0.437500000,0.312500000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_25061.1:
> HL_25061.1  6MWN U  624 G  632
UGUGAGAGG
> HL_25061.1  8CRE C 1343 G 1353
CUGUUUUGACG