Alignment of HL_20535.2 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
2
I

12
2

6
13
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
HL_20535.2_Instance_1 HL_20535.2,HL_5VOE_001,G15_C22GAUAAUAC
HL_20535.2_Sequence_1 HL_20535.25VOE_G15_C22GAUAAUACtrue98000.18
HL_20535.2_Instance_2 HL_20535.2,HL_8P9A_235,U715_G723UCCUUGUGG
HL_20535.2_Sequence_2 HL_20535.28P9A_U715_G723UCCUUGUGGtrue92000.74
HL_20535.2_Instance_3 HL_20535.2,HL_6GSK_204,G53_C61GUUCGACUC
HL_20535.2_Sequence_3 HL_20535.26GSK_G53_C61GUUCGACUCtrue100000.00

Conserved interactions between motif group positions in HL_20535.2:
1 2 s35 
1 6 cWW 
2 3 s35
JAR3D SCFG/MRF model for HL_20535.2:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.010138447,0.017999390,0.012030637,0.145215023,0.000000000],[0.111154629,0.015527922,0.148017973,0.014062841,0.000000000],[0.012052549,0.169605488,0.002470680,0.022513399,0.000000000],[0.159661783,0.013947978,0.134332446,0.011268815,0.000000000],[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 [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [6] // Basepair G15 - C22 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A16:U20
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A16
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U17
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[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 A19
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U20
Insertion    | Location [2] | Length Distribution [0.005372012,0.333064733,0.650013430,0.011012624,0.000537201] | Letter Distribution [0.214285714,0.214285714,0.214285714,0.357142857,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Insertion    | Location [3] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3
Sequences of instances from HL_20535.2:
> HL_20535.2  5VOE G   15 C   22
GAUAAUAC
> HL_20535.2  8P9A U  715 G  723
UCCUUGUGG
> HL_20535.2  6GSK G   53 C   61
GUUCGACUC