Alignment of HL_52953.3 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
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_52953.3_Instance_1 HL_52953.3,HL_4XWF_001,G24_C29GGAAAC
HL_52953.3_Sequence_1 HL_52953.34XWF_G24_C29GGAAACtrue100000.00
HL_52953.3_Instance_2 HL_52953.3,HL_8VVJ_001,G24_C29GGAAAC
HL_52953.3_Sequence_2 HL_52953.38VVJ_G24_C29GGAAACtrue100000.00
HL_52953.3_Instance_3 HL_52953.3,HL_6U8D_001,G161_C166GAGUAC
HL_52953.3_Sequence_3 HL_52953.36U8D_G161_C166GAGUACtrue78002.09
HL_52953.3_Instance_4 HL_52953.3,HL_3ADD_003,C47D_G47ICGAGUG
HL_52953.3_Sequence_4 HL_52953.33ADD_C47D_G47ICGAGUGtrue85001.42
HL_52953.3_Instance_5 HL_52953.3,HL_8UO6_006,C49_G54CAAUGG
HL_52953.3_Sequence_5 HL_52953.38UO6_C49_G54CAAUGGtrue84001.53
HL_52953.3_Instance_6 HL_52953.3,HL_8UO6_002,C49_G54CAAUGG
HL_52953.3_Sequence_6 HL_52953.38UO6_C49_G54CAAUGGtrue84001.53
HL_52953.3_Instance_7 HL_52953.3,HL_4KR9_002,G19_C24GGAAAC
HL_52953.3_Sequence_7 HL_52953.34KR9_G19_C24GGAAACtrue100000.00
HL_52953.3_Instance_8 HL_52953.3,HL_2QUS_003,C42_G47CGUGAG
HL_52953.3_Sequence_8 HL_52953.32QUS_C42_G47CGUGAGtrue90000.91
HL_52953.3_Instance_9 HL_52953.3,HL_2QUW_003,C42_G47CGUGAG
HL_52953.3_Sequence_9 HL_52953.32QUW_C42_G47CGUGAGtrue90000.91

Conserved interactions between motif group positions in HL_52953.3:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
4 5 s35
JAR3D SCFG/MRF model for HL_52953.3:
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 [0.0000244705618206] | Pair Probability [[0.009006118,0.017321707,0.010309555,0.187075879,0.000000000],[0.017652131,0.009019160,0.238952446,0.012694291,0.000000000],[0.010322369,0.229163838,0.001955353,0.023331249,0.000000000],[0.187344078,0.012641879,0.023675205,0.009534743,0.000000000],[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 [6] // Basepair G24 - C29 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G25:A28
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.318181818,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.590909091,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G25
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.590909091,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.227272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A26
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.318181818,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.318181818,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.318181818,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A27
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.590909091,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.227272727,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A28
Sequences of instances from HL_52953.3:
> HL_52953.3  4XWF G   24 C   29
GGAAAC
> HL_52953.3  8VVJ G   24 C   29
GGAAAC
> HL_52953.3  6U8D G  161 C  166
GAGUAC
> HL_52953.3  3ADD C  47D G  47I
CGAGUG
> HL_52953.3  8UO6 C   49 G   54
CAAUGG
> HL_52953.3  8UO6 C   49 G   54
CAAUGG
> HL_52953.3  4KR9 G   19 C   24
GGAAAC
> HL_52953.3  2QUS C   42 G   47
CGUGAG
> HL_52953.3  2QUW C   42 G   47
CGUGAG