Alignment of HL_72451.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_72451.4
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
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_72451.4_Instance_1 HL_72451.4_HL_4Y4O_130_G978_C985GGAACAAC
HL_72451.4_Sequence_1 HL_72451.4_HL_4Y4O_130_G978_C985GGAACAACtrue100000.00
HL_72451.4_Instance_2 HL_72451.4_HL_4V9F_029_G1076_C1083GGAACAAC
HL_72451.4_Sequence_2 HL_72451.4_HL_4V9F_029_G_1076_C_1083GGAACAACtrue100000.00
HL_72451.4_Instance_3 HL_72451.4_HL_7A0S_027_G989_C996GAAACAAC
HL_72451.4_Sequence_3 HL_72451.4_HL_7A0S_027_G989_C996GAAACAACtrue100000.00
HL_72451.4_Instance_4 HL_72451.4_HL_5J7L_160_G978_C985GAAACAAC
HL_72451.4_Sequence_4 HL_72451.4_HL_5J7L_160_G978_C985GAAACAACtrue100000.00
HL_72451.4_Instance_5 HL_72451.4_HL_4WF9_028_G1022_C1029GAAACAGC
HL_72451.4_Sequence_5 HL_72451.4_HL_4WF9_028_G_1022_C_1029GAAACAGCtrue88001.30
HL_72451.4_Instance_6 HL_72451.4_HL_5TBW_026_G1148_C1155GGAUGAAC
HL_72451.4_Sequence_6 HL_72451.4_HL_5TBW_026_G_1148_C_1155GGAUGAACtrue74002.85

Conserved interactions between motif group positions in HL_72451.4:
1 2 s35 
1 8 cWW 
2 5 s33 
2 8 s55 
3 4 s35 
4 5 perp 
6 7 s35 
5 4 7BPh
8 7 7BPh
JAR3D SCFG/MRF model for HL_72451.4:
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 [8] // Initial node G978 - C985 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003679589,0.053642867,0.004190070,0.076104487,0.000000000],[0.006463298,0.025257446,0.076749356,0.005021698,0.000000000],[0.004143537,0.609465400,0.000789802,0.010117932,0.000000000],[0.075130495,0.036484266,0.008868823,0.003890933,0.000000000],[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 [8] // Basepair G978 - C985 cWW 
HairpinNode  | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G979:A984
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G979
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A980
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A981
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.011363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.806818182,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.170454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.011363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C982
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A983
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A984
Sequences of instances from HL_72451.4:
> HL_72451.4 HL_4Y4O_130 G  978 C  985
GGAACAAC
> HL_72451.4 HL_4V9F_029 G 1076 C 1083
GGAACAAC
> HL_72451.4 HL_7A0S_027 G  989 C  996
GAAACAAC
> HL_72451.4 HL_5J7L_160 G  978 C  985
GAAACAAC
> HL_72451.4 HL_4WF9_028 G 1022 C 1029
GAAACAGC
> HL_72451.4 HL_5TBW_026 G 1148 C 1155
GGAUGAAC