Alignment of HL_66171.2 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
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_66171.2_Instance_1 HL_66171.2_HL_4Y4O_142_C1612_G1619CGACACAG
HL_66171.2_Sequence_1 HL_66171.2_HL_4Y4O_142_C_1612_G_1619CGACACAGtrue100000.00
HL_66171.2_Instance_2 HL_66171.2_HL_7A0S_040_C1628_G1635CGACACAG
HL_66171.2_Sequence_2 HL_66171.2_HL_7A0S_040_C_1628_G_1635CGACACAGtrue100000.00
HL_66171.2_Instance_3 HL_66171.2_HL_4WF9_038_C1656_G1663CGACACAG
HL_66171.2_Sequence_3 HL_66171.2_HL_4WF9_038_C_1656_G_1663CGACACAGtrue100000.00
HL_66171.2_Instance_4 HL_66171.2_HL_4V9F_042_C1687_G1694CGACACAG
HL_66171.2_Sequence_4 HL_66171.2_HL_4V9F_042_C_1687_G_1694CGACACAGtrue100000.00
HL_66171.2_Instance_5 HL_66171.2_HL_5TBW_041_C1844_G1851CGCAGCAG
HL_66171.2_Sequence_5 HL_66171.2_HL_5TBW_041_C_1844_G_1851CGCAGCAGtrue78003.30

Conserved interactions between motif group positions in HL_66171.2:
1 2 s35 
1 5 cWW 
2 4 s33 
2 5 s55 
3 4 s35 
4 3 7BPh
2 4 6BR
JAR3D SCFG/MRF model for HL_66171.2:
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 C1612 - G1619 from junction 
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [5] // Basepair C1612 - G1619 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G1613:C1617
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.018518519,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.944444444,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.018518519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1613
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.642857143,0.000000000,0.000000000,0.000000000],[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 C1615
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.013513514,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.959459459,0.000000000,0.000000000,0.000000000],[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 C1617
Insertion    | Location [1] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.642857143,0.214285714,0.071428571,0.071428571,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [2] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.642857143,0.071428571,0.214285714,0.071428571,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_66171.2:
> HL_66171.2 HL_4Y4O_142 C 1612 G 1619
CGACACAG
> HL_66171.2 HL_7A0S_040 C 1628 G 1635
CGACACAG
> HL_66171.2 HL_4WF9_038 C 1656 G 1663
CGACACAG
> HL_66171.2 HL_4V9F_042 C 1687 G 1694
CGACACAG
> HL_66171.2 HL_5TBW_041 C 1844 G 1851
CGCAGCAG