Alignment of HL_80709.3 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
2
I

10
2

5
11
1
I


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Alignment
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HL_80709.3_Instance_1 HL_80709.3,HL_4V9F_046,C1808_G1812CGCAG
HL_80709.3_Sequence_1 HL_80709.34V9F_C_1808_G_1812CGCAGtrue100000.00
HL_80709.3_Instance_2 HL_80709.3,HL_9DFE_042,C1752_G1756CGCAG
HL_80709.3_Sequence_2 HL_80709.39DFE_C_1752_G_1756CGCAGtrue100000.00
HL_80709.3_Instance_3 HL_80709.3,HL_7A0S_044,C1743_G1747CGCAG
HL_80709.3_Sequence_3 HL_80709.37A0S_C_1743_G_1747CGCAGtrue100000.00
HL_80709.3_Instance_4 HL_80709.3,HL_4WF9_042,C1779_G1783CGCAG
HL_80709.3_Sequence_4 HL_80709.34WF9_C_1779_G_1783CGCAGtrue100000.00
HL_80709.3_Instance_5 HL_80709.3,HL_5J7L_177,C1752_G1756CGAAG
HL_80709.3_Sequence_5 HL_80709.35J7L_C_1752_G_1756CGAAGtrue96000.37
HL_80709.3_Instance_6 HL_80709.3,HL_4ZNP_001,G26_C31GGAAAC
HL_80709.3_Sequence_6 HL_80709.34ZNP_G26_C31GGAAACtrue72002.67
HL_80709.3_Instance_7 HL_80709.3,HL_3IVK_002,C40_G44CGAAG
HL_80709.3_Sequence_7 HL_80709.33IVK_C40_G44CGAAGtrue96000.37
HL_80709.3_Instance_8 HL_80709.3,HL_3HHN_007,C40_G44CGAAG
HL_80709.3_Sequence_8 HL_80709.33HHN_C40_G44CGAAGtrue96000.37
HL_80709.3_Instance_9 HL_80709.3,HL_5MGA_001,C-11_G-6CUGUUG
HL_80709.3_Sequence_9 HL_80709.35MGA_C-11_G-6CUGUUGtrue54004.41
HL_80709.3_Instance_10 HL_80709.3,HL_5XH7_001,C-11_G-6CUCUUG
HL_80709.3_Sequence_10 HL_80709.35XH7_C-11_G-6CUCUUGtrue69002.95
HL_80709.3_Instance_11 HL_80709.3,HL_5KK5_001,C-11_G-6CUCUUG
HL_80709.3_Sequence_11 HL_80709.35KK5_C-11_G-6CUCUUGtrue69002.95

Conserved interactions between motif group positions in HL_80709.3:
1 2 s35 
1 5 cWW 
2 4 s33 
2 5 s55 
3 4 s35 
2 5 6BPh
JAR3D SCFG/MRF model for HL_80709.3:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000035196243062] | Pair Probability [[0.008779809,0.015979629,0.010084616,0.182882766,0.000000000],[0.018366806,0.008911187,0.281624635,0.012630157,0.000000000],[0.010177188,0.196105522,0.001920275,0.021839130,0.000000000],[0.184820392,0.012251502,0.024324066,0.009302320,0.000000000],[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 [0.633943052,0.364188787,0.001786044,0.000082117] | Right Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000] | Left Index [1] | Right Index [5] // Basepair C1808 - G1812 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G1809:A1811
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.006329114,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.006329114,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.715189873,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.272151899,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1809
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.346153846,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.115384615,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1810
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.653846154,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.269230769,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1811
Sequences of instances from HL_80709.3:
> HL_80709.3  4V9F C 1808 G 1812
CGCAG
> HL_80709.3  9DFE C 1752 G 1756
CGCAG
> HL_80709.3  7A0S C 1743 G 1747
CGCAG
> HL_80709.3  4WF9 C 1779 G 1783
CGCAG
> HL_80709.3  5J7L C 1752 G 1756
CGAAG
> HL_80709.3  4ZNP G   26 C   31
GGAAAC
> HL_80709.3  3IVK C   40 G   44
CGAAG
> HL_80709.3  3HHN C   40 G   44
CGAAG
> HL_80709.3  5MGA C  -11 G   -6
CUGUUG
> HL_80709.3  5XH7 C  -11 G   -6
CUCUUG
> HL_80709.3  5KK5 C  -11 G   -6
CUCUUG