Alignment of HL_69774.3 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
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_69774.3_Instance_1 HL_69774.3_HL_6DB9_001_G23_C29GAAACAC
HL_69774.3_Sequence_1 HL_69774.3_HL_6DB9_001_G23_C29GAAACACtrue100000.00
HL_69774.3_Instance_2 HL_69774.3_HL_4KZD_001_G37_C43GAAACAC
HL_69774.3_Sequence_2 HL_69774.3_HL_4KZD_001_G37_C43GAAACACtrue100000.00
HL_69774.3_Instance_3 HL_69774.3_HL_3IVK_003_G59_C65GAAACAC
HL_69774.3_Sequence_3 HL_69774.3_HL_3IVK_003_G59_C65GAAACACtrue100000.00
HL_69774.3_Instance_4 HL_69774.3_HL_3IGI_009_C368_G373CGAACG
HL_69774.3_Sequence_4 HL_69774.3_HL_3IGI_009_C368_G373CGAACGtrue72002.62
HL_69774.3_Instance_5 HL_69774.3_HL_6OL3_001_G64_C70GAACCCC
HL_69774.3_Sequence_5 HL_69774.3_HL_6OL3_001_G64_C70GAACCCCtrue73002.57

Conserved interactions between motif group positions in HL_69774.3:
1 2 s33 
1 6 cWW 
2 5 tSW 
3 4 s35 
4 5 s35 
5 6 s35 
4 3 7BPh
JAR3D SCFG/MRF model for HL_69774.3:
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 [6] // Initial node G23 - C29 from junction 
BasepairNode | Deletion Probability [0.0000003483978778] | Pair Probability [[0.009417290,0.019076634,0.010743958,0.195076917,0.000000000],[0.017226610,0.009304766,0.207905455,0.013002891,0.000000000],[0.010672216,0.239916288,0.002029679,0.025359511,0.000000000],[0.193575287,0.013296343,0.023433726,0.009962428,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Left Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | 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 [6] // Basepair G23 - C29 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.203107741,0.046494307,0.003483177,0.010868727,0.000000000],[0.145237611,0.015974221,0.033903959,0.009508809,0.000000000],[0.140766888,0.186788362,0.003483177,0.007980206,0.000000000],[0.155220156,0.012097436,0.013661963,0.011423258,0.000000000],[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 [2] | Right Index [5] // Basepair A25 - A28 tSW 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A26:C27
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A26
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.202702703,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.770270270,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C27
Sequences of instances from HL_69774.3:
> HL_69774.3 HL_6DB9_001 G   23 C   29
GAAACAC
> HL_69774.3 HL_4KZD_001 G   37 C   43
GAAACAC
> HL_69774.3 HL_3IVK_003 G   59 C   65
GAAACAC
> HL_69774.3 HL_3IGI_009 C  368 G  373
CGAACG
> HL_69774.3 HL_6OL3_001 G   64 C   70
GAACCCC