Alignment of HL_32617.1 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
2
I

10
2

5
11
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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Alignment
score
deficit
HL_32617.1_Instance_1 HL_32617.1_HL_3AM1_005_U18_A23UUGGUA
HL_32617.1_Sequence_1 HL_32617.1_HL_3AM1_005_U18_A23UUGGUAtrue99000.14
HL_32617.1_Instance_2 HL_32617.1_HL_3AM1_001_U18_A23UUGGUA
HL_32617.1_Sequence_2 HL_32617.1_HL_3AM1_001_U18_A23UUGGUAtrue99000.14
HL_32617.1_Instance_3 HL_32617.1_HL_3W3S_005_C15_G20ACUGGUG
HL_32617.1_Sequence_3 HL_32617.1_HL_3W3S_005_C15_G20ACUGGUGtrue99000.13
HL_32617.1_Instance_4 HL_32617.1_HL_3W3S_001_C15_G20ACUGGUG
HL_32617.1_Sequence_4 HL_32617.1_HL_3W3S_001_C15_G20ACUGGUGtrue99000.13
HL_32617.1_Instance_5 HL_32617.1_HL_4ZDO_001_G15_C20AGUGGUC
HL_32617.1_Sequence_5 HL_32617.1_HL_4ZDO_001_G15_C20AGUGGUCtrue100000.00
HL_32617.1_Instance_6 HL_32617.1_HL_3RG5_009_G15_C20AGUGGUC
HL_32617.1_Sequence_6 HL_32617.1_HL_3RG5_009_G15_C20AGUGGUCtrue100000.00
HL_32617.1_Instance_7 HL_32617.1_HL_3RG5_005_G15_C20AGUGGUC
HL_32617.1_Sequence_7 HL_32617.1_HL_3RG5_005_G15_C20AGUGGUCtrue100000.00
HL_32617.1_Instance_8 HL_32617.1_HL_3ADD_001_G15_C20AGUGGUC
HL_32617.1_Sequence_8 HL_32617.1_HL_3ADD_001_G15_C20AGUGGUCtrue100000.00
HL_32617.1_Instance_9 HL_32617.1_HL_5F9R_004_G105_C109GAGUC
HL_32617.1_Sequence_9 HL_32617.1_HL_5F9R_004_G105_C109GAGUCtrue62003.61

Conserved interactions between motif group positions in HL_32617.1:
1 2 s35 
1 5 cWW 
3 4 cSH 
JAR3D SCFG/MRF model for HL_32617.1:
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 [5] // Initial node U18 - A23 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008922170,0.017743555,0.010103043,0.186825820,0.000000000],[0.017689168,0.009026441,0.208316861,0.012070633,0.000000000],[0.010068672,0.237156075,0.001945841,0.023587200,0.000000000],[0.206056080,0.012088270,0.028846556,0.009553614,0.000000000],[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 [5] // Basepair U18 - A23 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U19:U22
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.074204418,0.075610898,0.004157321,0.073893488,0.000000000],[0.055398446,0.083486430,0.000920502,0.074048396,0.000000000],[0.064832555,0.000920502,0.079084665,0.174618960,0.000000000],[0.075355769,0.074903398,0.000920502,0.087643751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G21 - U22 cSH 
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.136363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.772727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U19
Insertion    | Location [1] | Length Distribution [0.114812666,0.880026871,0.004916181,0.000244282] | Letter Distribution [0.050000000,0.050000000,0.850000000,0.050000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_32617.1:
> HL_32617.1 HL_3AM1_005 U   18 A   23
UUGGUA
> HL_32617.1 HL_3AM1_001 U   18 A   23
UUGGUA
> HL_32617.1 HL_3W3S_005 C   15 G  20A
CUGGUG
> HL_32617.1 HL_3W3S_001 C   15 G  20A
CUGGUG
> HL_32617.1 HL_4ZDO_001 G   15 C  20A
GUGGUC
> HL_32617.1 HL_3RG5_009 G   15 C  20A
GUGGUC
> HL_32617.1 HL_3RG5_005 G   15 C  20A
GUGGUC
> HL_32617.1 HL_3ADD_001 G   15 C  20A
GUGGUC
> HL_32617.1 HL_5F9R_004 G  105 C  109
GAGUC