Alignment of HL_79272.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_79272.2
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
edit
distance

Alignment
score
deficit
HL_79272.2_Instance_1 HL_79272.2_HL_4WF9_042_C1779_G1783CGCAG
HL_79272.2_Sequence_1 HL_79272.2_HL_4WF9_042_C_1779_G_1783CGCAGtrue100000.00
HL_79272.2_Instance_2 HL_79272.2_HL_5J7L_177_C1752_G1756CGAAG
HL_79272.2_Sequence_2 HL_79272.2_HL_5J7L_177_C_1752_G_1756CGAAGtrue96000.37
HL_79272.2_Instance_3 HL_79272.2_HL_4V9F_046_C1808_G1812CGCAG
HL_79272.2_Sequence_3 HL_79272.2_HL_4V9F_046_C_1808_G_1812CGCAGtrue100000.00
HL_79272.2_Instance_4 HL_79272.2_HL_4Y4O_146_C1752_G1756CGCAG
HL_79272.2_Sequence_4 HL_79272.2_HL_4Y4O_146_C_1752_G_1756CGCAGtrue100000.00
HL_79272.2_Instance_5 HL_79272.2_HL_7A0S_044_C1743_G1747CGCAG
HL_79272.2_Sequence_5 HL_79272.2_HL_7A0S_044_C_1743_G_1747CGCAGtrue100000.00
HL_79272.2_Instance_6 HL_79272.2_HL_3IVK_002_C40_G44CGAAG
HL_79272.2_Sequence_6 HL_79272.2_HL_3IVK_002_C40_G44CGAAGtrue96000.37
HL_79272.2_Instance_7 HL_79272.2_HL_3HHN_007_C40_G44CGAAG
HL_79272.2_Sequence_7 HL_79272.2_HL_3HHN_007_C40_G44CGAAGtrue96000.37
HL_79272.2_Instance_8 HL_79272.2_HL_5MGA_001_C-11_G-6CUGUUG
HL_79272.2_Sequence_8 HL_79272.2_HL_5MGA_001_C-11_G-6CUGUUGtrue54004.41
HL_79272.2_Instance_9 HL_79272.2_HL_4ZNP_001_G26_C31GGAAAC
HL_79272.2_Sequence_9 HL_79272.2_HL_4ZNP_001_G26_C31GGAAACtrue72002.67
HL_79272.2_Instance_10 HL_79272.2_HL_5XH7_001_C-11_G-6CUCUUG
HL_79272.2_Sequence_10 HL_79272.2_HL_5XH7_001_C-11_G-6CUCUUGtrue69002.95
HL_79272.2_Instance_11 HL_79272.2_HL_5KK5_001_C-11_G-6CUCUUG
HL_79272.2_Sequence_11 HL_79272.2_HL_5KK5_001_C-11_G-6CUCUUGtrue69002.95

Conserved interactions between motif group positions in HL_79272.2:
1 2 s35 
1 5 cWW 
2 4 s33 
2 5 s55 
3 4 s35 
2 5 6BPh
JAR3D SCFG/MRF model for HL_79272.2:
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 C1779 - G1783 from junction 
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 C1779 - G1783 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G1780:A1782
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 G1780
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 C1781
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 A1782
Sequences of instances from HL_79272.2:
> HL_79272.2 HL_4WF9_042 C 1779 G 1783
CGCAG
> HL_79272.2 HL_5J7L_177 C 1752 G 1756
CGAAG
> HL_79272.2 HL_4V9F_046 C 1808 G 1812
CGCAG
> HL_79272.2 HL_4Y4O_146 C 1752 G 1756
CGCAG
> HL_79272.2 HL_7A0S_044 C 1743 G 1747
CGCAG
> HL_79272.2 HL_3IVK_002 C   40 G   44
CGAAG
> HL_79272.2 HL_3HHN_007 C   40 G   44
CGAAG
> HL_79272.2 HL_5MGA_001 C  -11 G   -6
CUGUUG
> HL_79272.2 HL_4ZNP_001 G   26 C   31
GGAAAC
> HL_79272.2 HL_5XH7_001 C  -11 G   -6
CUCUUG
> HL_79272.2 HL_5KK5_001 C  -11 G   -6
CUCUUG