Alignment of HL_02483.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_02483.1
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
5

2
5
5
I

6
6

3
7
6
I

8
6

4
9
6
I

10
6

5
11
6
I

12
6

6
13
6
I

14
6

7
15
5
I

16
5

8
17
4
I

18
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_02483.1_Instance_1 HL_02483.1_HL_4PKD_002_U92_G103UGAUCACGAAGG
HL_02483.1_Sequence_1 HL_02483.1_HL_4PKD_002_U92_G103UGAUCACGAAGGtrue100000.00

Conserved interactions between motif group positions in HL_02483.1:
1 10 cWW 
2 8 tWH 
2 9 s55 
3 4 cSH 
5 6 s33 
7 8 s35 
8 9 s35 
9 10 s35 
6 6 2BPh
2 8 7BPh
4 3 7BR
JAR3D SCFG/MRF model for HL_02483.1:
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 [10] // Initial node U92 - G103 from junction 
BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.011357495,0.014122426,0.014418960,0.037643649,0.000000000],[0.305533580,0.028227484,0.042773463,0.016192886,0.000000000],[0.014734624,0.037492866,0.003338882,0.014817277,0.000000000],[0.087046211,0.014824487,0.343789173,0.013686536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U92 - G103 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.500586469,0.004906855,0.432872759,0.004906855,0.000000000],[0.005999965,0.002974708,0.000700979,0.000700979,0.000000000],[0.000700979,0.001736421,0.025766190,0.007503062,0.000000000],[0.003167529,0.000700979,0.003359793,0.003415476,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair A94 - A101 tWH 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U95:A100
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.091584266,0.098148224,0.008532723,0.093469509,0.000000000],[0.093695846,0.095862018,0.001090000,0.012308576,0.000000000],[0.013771314,0.001090000,0.099428981,0.088695882,0.000000000],[0.093537464,0.118900979,0.001090000,0.088794218,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U95 - C96 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C98
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G99
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A100
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_02483.1:
> HL_02483.1 HL_4PKD_002 U   92 G  103
UGAUCACGAAGG