Alignment of HL_70970.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_70970.1
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_70970.1_Instance_1 HL_70970.1_HL_4V9F_004_U125_A129UCUAA
HL_70970.1_Sequence_1 HL_70970.1_HL_4V9F_004_U125_A129UCUAAtrue100000.00
HL_70970.1_Instance_2 HL_70970.1_HL_5J7L_163_G1171_C1178GCUUAUGC
HL_70970.1_Sequence_2 HL_70970.1_HL_5J7L_163_G_1171_C_1178GCUUAUGCtrue73002.59

Conserved interactions between motif group positions in HL_70970.1:
1 2 perp 
1 5 cWW 
2 4 perp 
4 5 s35 
JAR3D SCFG/MRF model for HL_70970.1:
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 U125 - A129 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009384013,0.018908278,0.010497082,0.198820958,0.000000000],[0.019570724,0.009688269,0.200004160,0.012164451,0.000000000],[0.010445199,0.211498280,0.002066765,0.024906359,0.000000000],[0.211388534,0.012081037,0.038377715,0.010198176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair U125 - A129 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node C126:A128
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C126
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U127
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A128
Insertion    | Location [1] | Length Distribution [0.481347774,0.012033694,0.012635379,0.481347774,0.012033694,0.000601685] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_70970.1:
> HL_70970.1 HL_4V9F_004 U  125 A  129
UCUAA
> HL_70970.1 HL_5J7L_163 G 1171 C 1178
GCUUAUGC