Cluster CL6
Cluster summary
| Number.of.reads |
Number.of.pairs |
Density |
| 8946
|
382743
|
0.0096
|
|
Summary of RepeatMasker hits
| |
class.fammily |
class |
family |
hits |
hits[%] |
content |
Mean_Score |
| 3
|
LTR/Copia
|
LTR
|
Copia
|
63
|
0.704
|
0.4675
|
245
|
| 4
|
DNA/MULE-MuDR
|
DNA
|
MULE-MuDR
|
8
|
0.089
|
0.0631
|
229
|
| 5
|
Low_complexity
|
Low_complexity
|
Low_complexity
|
7
|
0.078
|
0.0250
|
27
|
| 6
|
DNA
|
DNA
|
DNA
|
3
|
0.034
|
0.0101
|
227
|
| 7
|
Simple_repeat
|
Simple_repeat
|
Simple_repeat
|
1
|
0.011
|
0.0034
|
231
|
|
Summary of RepeatMasker custom library hits
| |
class.fammily |
class |
family |
hits |
hits[%] |
content |
Mean_Score |
| 3
|
DNA/DCRE12/DCRE12
|
DNA
|
DCRE12
|
1936
|
21.600
|
20.2624
|
658
|
| 4
|
DNA/3Mb1
|
DNA
|
3Mb1
|
1857
|
20.800
|
19.3825
|
629
|
| 5
|
DNA/DCRE7/DCRE7
|
DNA
|
DCRE7
|
1279
|
14.300
|
13.6614
|
734
|
| 6
|
DNA/DCRE3/DCRE3
|
DNA
|
DCRE3
|
545
|
6.090
|
5.6286
|
714
|
| 7
|
DNA/DCRE13/DCRE13
|
DNA
|
DCRE13
|
491
|
5.490
|
5.2601
|
634
|
| 8
|
DNA/DCRE15/DCRE15
|
DNA
|
DCRE15
|
422
|
4.720
|
3.8724
|
542
|
| 9
|
DNA/CentromereRepeat
|
DNA
|
CentromereRepeat
|
3
|
0.034
|
0.0119
|
271
|
| 10
|
DNA/DCRE8/DCRE8
|
DNA
|
DCRE8
|
1
|
0.011
|
0.0056
|
392
|
| 11
|
DNA/Plastid_43501-44500
|
DNA
|
Plastid_43501-44500
|
1
|
0.011
|
0.0055
|
364
|
| 12
|
DNA/Plastid_72001-73000
|
DNA
|
Plastid_72001-73000
|
1
|
0.011
|
0.0050
|
382
|
| 13
|
DNA/DCRE20/DCRE20
|
DNA
|
DCRE20
|
1
|
0.011
|
0.0043
|
260
|
| 14
|
DNA/DCRE2/DCRE2
|
DNA
|
DCRE2
|
1
|
0.011
|
0.0041
|
318
|
| 15
|
DNA/DCRE1/DCRE1
|
DNA
|
DCRE1
|
1
|
0.011
|
0.0036
|
230
|
| 16
|
DNA/Plastid_20501-21500
|
DNA
|
Plastid_20501-21500
|
1
|
0.011
|
0.0032
|
247
|
|
Summary of TE domain hits
Number of similarity hits for individual sequences
| |
Domain |
ID |
Type |
Lineage |
Hits |
MeanScore |
| 1
|
Ty1-GAG
|
Wicker_Osr8_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
75
|
32
|
| 2
|
Ty1-GAG
|
Wicker_ATCopia43_At-1
|
Ty1/copia
|
Maximus/SIRE
|
60
|
34
|
| 3
|
Ty1-GAG
|
COPIA3-I_LC
|
Ty1/copia
|
Maximus/SIRE
|
22
|
32
|
| 4
|
Ty1-GAG
|
Copia-20_SB-I
|
Ty1/copia
|
Ivana/Oryco
|
10
|
31
|
| 5
|
Ty1-GAG
|
Wicker_Ivana_102J11-1
|
Ty1/copia
|
Ivana/Oryco
|
5
|
31
|
| 6
|
Ty1-GAG
|
Wicker_Marcus_Os-1
|
Ty1/copia
|
Maximus/SIRE
|
4
|
31
|
| 7
|
Ty1-GAG
|
Wicker_Echidne_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
1
|
30
|
| 8
|
Ty1-GAG
|
COP12_I_MT
|
Ty1/copia
|
Ivana/Oryco
|
1
|
31
|
| 9
|
Ty1-GAG
|
Copia41-PTR_I
|
Ty1/copia
|
Ivana/Oryco
|
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
|
CL3
|
629
|
| 2
|
CL26
|
406
|
| 3
|
CL54
|
7
|
| 4
|
CL16
|
1
|
| 5
|
CL12
|
1
|
|
reads with similarity to all other neighboring clusters
no mates information available