Alignment of HL_83632.1 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


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HL_83632.1_Instance_1 HL_83632.1,HL_2AKE_002,A31_U39ACUCCAGAU
HL_83632.1_Sequence_1 HL_83632.12AKE_A31_U39ACUCCAGAUtrue94000.92
HL_83632.1_Instance_2 HL_83632.1,HL_6UGG_005,C31_G39CCUGUCACG
HL_83632.1_Sequence_2 HL_83632.16UGG_C31_G39CCUGUCACGtrue90001.40
HL_83632.1_Instance_3 HL_83632.1,HL_1J1U_002,A532_U540ACUGUAGAU
HL_83632.1_Sequence_3 HL_83632.11J1U_A532_U540ACUGUAGAUtrue100000.00
HL_83632.1_Instance_4 HL_83632.1,HL_2ZNI_002,A31_U39ACUCUAAAU
HL_83632.1_Sequence_4 HL_83632.12ZNI_A31_U39ACUCUAAAUtrue100000.00
HL_83632.1_Instance_5 HL_83632.1,HL_4LCK_002,C30_G38CUUGCCAAG
HL_83632.1_Sequence_5 HL_83632.14LCK_C30_G38CUUGCCAAGtrue88001.74
HL_83632.1_Instance_6 HL_83632.1,HL_2IY5_002,A31_U39ACUGAAAAU
HL_83632.1_Sequence_6 HL_83632.12IY5_A31_U39ACUGAAAAUtrue98000.26

Conserved interactions between motif group positions in HL_83632.1:
1 2 s35 
1 8 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35
JAR3D SCFG/MRF model for HL_83632.1:
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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009013987,0.019605318,0.009876744,0.232440278,0.000000000],[0.017741822,0.009261230,0.210457091,0.011068706,0.000000000],[0.009903856,0.191310627,0.001979717,0.041664037,0.000000000],[0.190340243,0.011336542,0.023349813,0.010649987,0.000000000],[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 [8] // Basepair A31 - U39 cWW 
HairpinNode  | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node C32:A38
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.687500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C32
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.562500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C35
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A36
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G37
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A38
Insertion    | Location [1] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_83632.1:
> HL_83632.1  2AKE A   31 U   39
ACUCCAGAU
> HL_83632.1  6UGG C   31 G   39
CCUGUCACG
> HL_83632.1  1J1U A  532 U  540
ACUGUAGAU
> HL_83632.1  2ZNI A   31 U   39
ACUCUAAAU
> HL_83632.1  4LCK C   30 G   38
CUUGCCAAG
> HL_83632.1  2IY5 A   31 U   39
ACUGAAAAU