Alignment of HL_83808.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_83808.4
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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_83808.4_Instance_1 HL_83808.4,HL_3NKB_001,C20_G28CUCCUCGCG
HL_83808.4_Sequence_1 HL_83808.43NKB_C20_G28CUCCUCGCGtrue100000.00
HL_83808.4_Instance_2 HL_83808.4,HL_4PR6_001,C119_G128CUCCUCGCUG
HL_83808.4_Sequence_2 HL_83808.44PR6_C119_G128CUCCUCGCUGtrue98000.36
HL_83808.4_Instance_3 HL_83808.4,HL_4PRF_001,C119_G128CUCCUCGCUG
HL_83808.4_Sequence_3 HL_83808.44PRF_C119_G128CUCCUCGCUGtrue98000.36

Conserved interactions between motif group positions in HL_83808.4:
1 2 s35 
1 7 cWW 
2 5 s35 
2 6 tWW 
2 7 s55 
3 4 s35 
5 6 s53 
6 7 s55 
5 4 7BPh
5 2 7BR
JAR3D SCFG/MRF model for HL_83808.4:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000000035094402] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.005372012,0.333064733,0.650013430,0.011012624,0.000537201] | Right Letter Distribution [0.071428571,0.500000000,0.071428571,0.357142857,0.000000000] | Left Index [1] | Right Index [7] // Basepair C20 - G28 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.015976020,0.013094388,0.002897389,0.014283421,0.000000000],[0.265966666,0.013684298,0.012208598,0.013474981,0.000000000],[0.002897389,0.009411803,0.025465123,0.013405938,0.000000000],[0.232094355,0.014007523,0.318865086,0.032267022,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair U21 - G26 tWW 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [0.999999999999999] // Hairpin node C22:C25
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C22
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C23
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.934782609,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.021739130,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25
Insertion    | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_83808.4:
> HL_83808.4  3NKB C   20 G   28
CUCCUCGCG
> HL_83808.4  4PR6 C  119 G  128
CUCCUCGCUG
> HL_83808.4  4PRF C  119 G  128
CUCCUCGCUG