Cluster CL5
Cluster summary
| Number.of.reads |
Number.of.pairs |
Density |
| 9538
|
308780
|
0.0068
|
|
Summary of RepeatMasker hits
| |
class.fammily |
class |
family |
hits |
hits[%] |
content |
Mean_Score |
| 3
|
Low_complexity
|
Low_complexity
|
Low_complexity
|
270
|
2.830
|
1.7211
|
48
|
| 4
|
LTR/Copia
|
LTR
|
Copia
|
21
|
0.220
|
0.1672
|
237
|
| 5
|
Simple_repeat
|
Simple_repeat
|
Simple_repeat
|
3
|
0.032
|
0.0085
|
197
|
|
Summary of RepeatMasker custom library hits
| |
class.fammily |
class |
family |
hits |
hits[%] |
content |
Mean_Score |
| 3
|
DNA/DCRE4/DCRE4
|
DNA
|
DCRE4
|
1584
|
16.600
|
15.5857
|
679
|
| 4
|
DNA/DCRE19/DCRE19
|
DNA
|
DCRE19
|
1498
|
15.700
|
14.7573
|
710
|
| 5
|
DNA/DCRE18/DCRE18
|
DNA
|
DCRE18
|
1296
|
13.600
|
12.7540
|
696
|
| 6
|
DNA/DCRE22/DCRE22
|
DNA
|
DCRE22
|
967
|
10.100
|
9.6108
|
716
|
| 7
|
DNA/DCRE10/DCRE10
|
DNA
|
DCRE10
|
3
|
0.032
|
0.0162
|
241
|
| 8
|
DNA/3Mb1
|
DNA
|
3Mb1
|
2
|
0.021
|
0.0083
|
246
|
| 9
|
DNA/DCRE14/DCRE14
|
DNA
|
DCRE14
|
1
|
0.011
|
0.0059
|
245
|
| 10
|
DNA/CentromereRepeat
|
DNA
|
CentromereRepeat
|
1
|
0.011
|
0.0043
|
282
|
| 11
|
DNA/Plastid_136501-137500
|
DNA
|
Plastid_136501-137500
|
1
|
0.011
|
0.0043
|
340
|
| 12
|
DNA/DCRE8/DCRE8
|
DNA
|
DCRE8
|
1
|
0.011
|
0.0042
|
310
|
|
Summary of TE domain hits
Number of similarity hits for individual sequences
| |
Domain |
ID |
Type |
Lineage |
Hits |
MeanScore |
| 1
|
Ty1-INT
|
Wicker_Echidne_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
1
|
31
|
| 2
|
Ty1-INT
|
Wicker_Osr9_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
1
|
30
|
| 3
|
Ty1-GAG
|
Llorens_RTvr2_AY900122.1
|
Ty1/copia
|
Tork
|
1
|
30
|
|
Layout of the cluster
Connected component
Neighborhood of the cluster
Explore interactive graph - 1st order neighbors
Explore interactive graph - 2nd order neighbors
Clusters with similarity hits
| |
cluster |
number of similarity hits |
| 1
|
CL11
|
354
|
| 2
|
CL19
|
19
|
| 3
|
CL4
|
11
|
| 4
|
CL33
|
1
|
|
reads with similarity to all other neighboring clusters
no mates information available