Alignment of HL_49873.1 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
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
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Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_49873.1_Instance_1 HL_49873.1_HL_3ZGZ_001_G12_C23GGAAUCGGUAGAC
HL_49873.1_Sequence_1 HL_49873.1_HL_3ZGZ_001_G12_C23GGAAUCGGUAGACtrue94001.10
HL_49873.1_Instance_2 HL_49873.1_HL_2BTE_001_G12_C23GGAAUGGGUAGAC
HL_49873.1_Sequence_2 HL_49873.1_HL_2BTE_001_G12_C23GGAAUGGGUAGACtrue100000.00
HL_49873.1_Instance_3 HL_49873.1_HL_5AH5_005_G12_C23GAAAUCGGUAAAC
HL_49873.1_Sequence_3 HL_49873.1_HL_5AH5_005_G12_C23GAAAUCGGUAAACtrue84002.78

Conserved interactions between motif group positions in HL_49873.1:
1 2 s35 
1 8 cWW 
2 3 s35 
2 6 cWS 
2 7 tSH 
2 8 s55 
3 4 s35 
3 5 cWS 
5 6 s35 
7 8 s35 
8 7 7BPh
7 2 6BR
2 6 6BR
JAR3D SCFG/MRF model for HL_49873.1:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [8] // Initial node G12 - C23 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G12 - C23 cWW 
HairpinNode  | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [0.285362311623589] // Hairpin node G13:A22
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.246892522,0.200307206,0.211681907,0.204611433,0.000000000],[0.016004500,0.013053530,0.002177663,0.013247577,0.000000000],[0.021640765,0.002177663,0.027736420,0.010358648,0.000000000],[0.007774354,0.008200965,0.006489923,0.007644924,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A14 - A20A cWS 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.104754894,0.110429214,0.092008273,0.210537532,0.000000000],[0.025184133,0.022941046,0.002489079,0.022167953,0.000000000],[0.151236163,0.002489079,0.204982108,0.011956389,0.000000000],[0.010024486,0.010464037,0.008480656,0.009854957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G13 - G21 cWS 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.104355937,0.045189764,0.001019127,0.005611930,0.000000000],[0.093142996,0.061480989,0.001019127,0.001019127,0.000000000],[0.285637838,0.002759710,0.015709346,0.197413341,0.000000000],[0.093049013,0.090553501,0.001019127,0.001019127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G13 - A22 tSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A15
Insertion    | Location [3] | Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.029411765,0.147058824,0.441176471,0.382352941,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3
Sequences of instances from HL_49873.1:
> HL_49873.1 HL_3ZGZ_001 G   12 C   23
GGAAUCGGUAGAC
> HL_49873.1 HL_2BTE_001 G   12 C   23
GGAAUGGGUAGAC
> HL_49873.1 HL_5AH5_005 G   12 C   23
GAAAUCGGUAAAC