Alignment of HL_87553.1 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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


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HL_87553.1_Instance_1 HL_87553.1,HL_8P9A_133,G910_C918GCGAAAGAC
HL_87553.1_Sequence_1 HL_87553.18P9A_G910_C918GCGAAAGACtrue94000.59
HL_87553.1_Instance_2 HL_87553.1,HL_8CRE_020,G906_C914GCGAAAGAC
HL_87553.1_Sequence_2 HL_87553.18CRE_G906_C914GCGAAAGACtrue94000.59
HL_87553.1_Instance_3 HL_87553.1,HL_6CF2_001,A13_U20ACUUCGGU
HL_87553.1_Sequence_3 HL_87553.16CF2_A13_U20ACUUCGGUtrue84001.55
HL_87553.1_Instance_4 HL_87553.1,HL_9DFE_024,C884_G892CCCACCAG
HL_87553.1_Sequence_4 HL_87553.19DFE_C884_G892CCCACCAGtrue94000.57
HL_87553.1_Instance_5 HL_87553.1,HL_5H9F_001,G50_C57GCGCCAGC
HL_87553.1_Sequence_5 HL_87553.15H9F_G50_C57GCGCCAGCtrue100000.00
HL_87553.1_Instance_6 HL_87553.1,HL_4WZD_250,U47_A53UCAUCGA
HL_87553.1_Sequence_6 HL_87553.14WZD_U47_A53UCAUCGAtrue87001.26
HL_87553.1_Instance_7 HL_87553.1,HL_2CSX_002,U31_G39UCUCAUAAG
HL_87553.1_Sequence_7 HL_87553.12CSX_U31_G39UCUCAUAAGtrue59003.86

Conserved interactions between motif group positions in HL_87553.1:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 cWW 
3 4 s35 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_87553.1:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009301346,0.017901890,0.010665435,0.178273937,0.000000000],[0.056334118,0.011672122,0.179784817,0.012403488,0.000000000],[0.010674483,0.199370953,0.002144743,0.026513880,0.000000000],[0.184235701,0.012355948,0.077991634,0.010375505,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G910 - C918 cWW 
BasepairNode | Deletion Probability [0.0000011539492903] | Pair Probability [[0.009180555,0.014066805,0.011165747,0.101801611,0.000000000],[0.249026867,0.022481822,0.157873034,0.013154810,0.000000000],[0.011371937,0.103065547,0.002518406,0.017137505,0.000000000],[0.106447750,0.012307145,0.157536223,0.010864236,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.567476145,0.287777049,0.143585601,0.001110718,0.000050487] | Right Letter Distribution [0.250000000,0.083333333,0.416666667,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair C911 - A917 cWW 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G912:A915
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.388888889,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G912
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.388888889,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.388888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A914
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.277777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A915
Insertion    | Location [1] | Length Distribution [0.427699602,0.567912443,0.004186211,0.000201745] | Letter Distribution [0.416666667,0.250000000,0.083333333,0.250000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Insertion    | Location [2] | Length Distribution [0.850913138,0.147720949,0.001315324,0.000050589] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_87553.1:
> HL_87553.1  8P9A G  910 C  918
GCGAAAGAC
> HL_87553.1  8CRE G  906 C  914
GCGAAAGAC
> HL_87553.1  6CF2 A   13 U   20
ACUUCGGU
> HL_87553.1  9DFE C  884 G  892
CCCACCAG
> HL_87553.1  5H9F G   50 C   57
GCGCCAGC
> HL_87553.1  4WZD U   47 A   53
UCAUCGA
> HL_87553.1  2CSX U   31 G   39
UCUCAUAAG