Cluster CL9
Cluster summary
| Number.of.reads |
Number.of.pairs |
Density |
| 6662
|
429058
|
0.019
|
|
Summary of RepeatMasker hits
| |
class.fammily |
class |
family |
hits |
hits[%] |
content |
Mean_Score |
| 3
|
LTR/Copia
|
LTR
|
Copia
|
728
|
10.90
|
8.322
|
279
|
| 4
|
LTR/Gypsy
|
LTR
|
Gypsy
|
8
|
0.12
|
0.082
|
233
|
|
Summary of RepeatMasker custom library hits
| |
class.fammily |
class |
family |
hits |
hits[%] |
content |
Mean_Score |
| 3
|
DNA/DCRE17/DCRE17
|
DNA
|
DCRE17
|
2813
|
42.200
|
39.7782
|
666
|
| 4
|
DNA/DCRE1/DCRE1
|
DNA
|
DCRE1
|
1389
|
20.800
|
19.6491
|
659
|
| 5
|
DNA/DCRE21/DCRE21
|
DNA
|
DCRE21
|
756
|
11.300
|
10.4802
|
693
|
| 6
|
DNA/DCRE23/DCRE23
|
DNA
|
DCRE23
|
681
|
10.200
|
8.6300
|
647
|
| 7
|
DNA/DCRE5/DCRE5
|
DNA
|
DCRE5
|
566
|
8.500
|
6.8288
|
632
|
| 8
|
DNA/DCRE2/DCRE2
|
DNA
|
DCRE2
|
49
|
0.736
|
0.3020
|
247
|
| 9
|
DNA/DCRE4/DCRE4
|
DNA
|
DCRE4
|
28
|
0.420
|
0.2699
|
263
|
| 10
|
DNA/DCRE10/DCRE10
|
DNA
|
DCRE10
|
2
|
0.030
|
0.0107
|
296
|
| 11
|
DNA/Plastid_12501-13500
|
DNA
|
Plastid_12501-13500
|
1
|
0.015
|
0.0087
|
464
|
| 12
|
DNA/DCRE25/DCRE25
|
DNA
|
DCRE25
|
1
|
0.015
|
0.0070
|
270
|
| 13
|
DNA/Plastid_146001-147000
|
DNA
|
Plastid_146001-147000
|
1
|
0.015
|
0.0063
|
304
|
| 14
|
DNA/3Mb1
|
DNA
|
3Mb1
|
1
|
0.015
|
0.0043
|
248
|
|
Summary of TE domain hits
Number of similarity hits for individual sequences
| |
Domain |
ID |
Type |
Lineage |
Hits |
MeanScore |
| 1
|
Ty1-INT
|
Wicker_Maximus_cons
|
Ty1/copia
|
Maximus/SIRE
|
207
|
36
|
| 2
|
Ty1-INT
|
Wicker_Usier_11O9-1
|
Ty1/copia
|
Maximus/SIRE
|
176
|
44
|
| 3
|
Ty1-PROT
|
COPIA3-I_LC
|
Ty1/copia
|
Maximus/SIRE
|
101
|
35
|
| 4
|
Ty1-INT
|
Wicker_Echidne_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
67
|
41
|
| 5
|
Ty1-INT
|
Wicker_Marcus_Os-1
|
Ty1/copia
|
Maximus/SIRE
|
61
|
46
|
| 6
|
Ty1-INT
|
Wicker_ATCopia58_At-101
|
Ty1/copia
|
Maximus/SIRE
|
56
|
33
|
| 7
|
Ty1-INT
|
Wicker_Osr9_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
52
|
42
|
| 8
|
Ty1-INT
|
Copia-53_ZM-I
|
Ty1/copia
|
Ivana/Oryco
|
51
|
34
|
| 9
|
Ty1-INT
|
Copia-54_ZM-I
|
Ty1/copia
|
Ivana/Oryco
|
31
|
35
|
| 10
|
Ty1-INT
|
Wicker_Osr10_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
30
|
36
|
| 11
|
Ty1-INT
|
ATCOPIA43I
|
Ty1/copia
|
Maximus/SIRE
|
29
|
35
|
| 12
|
Ty1-PROT
|
Wicker_Maximus_cons
|
Ty1/copia
|
Maximus/SIRE
|
26
|
38
|
| 13
|
Ty1-PROT
|
Copia-49_ZM-I
|
Ty1/copia
|
Ivana/Oryco
|
23
|
35
|
| 14
|
Ty1-PROT
|
Copia-29_SB-I
|
Ty1/copia
|
Ivana/Oryco
|
23
|
35
|
| 15
|
Ty1-PROT
|
Wicker_Osr8_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
15
|
34
|
| 16
|
Ty1-PROT
|
Wicker_Osr10_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
15
|
31
|
| 17
|
Ty1-PROT
|
HOBS_I
|
Ty1/copia
|
unclass(Tork)
|
10
|
32
|
| 18
|
Ty1-INT
|
GmCOPIA11_I
|
Ty1/copia
|
Ivana/Oryco
|
4
|
33
|
| 19
|
Ty1-INT
|
Llorens_Oryco1-2_AL606630.3
|
Ty1/copia
|
Ivana/Oryco
|
4
|
31
|
| 20
|
Ty1-INT
|
CPSC3_I
|
Ty1/copia
|
Ivana/Oryco
|
4
|
31
|
| 21
|
Ty1-INT
|
SIRE1_INT_
|
Ty1/copia
|
Maximus/SIRE
|
3
|
44
|
| 22
|
Ty1-PROT
|
Wicker_ATCopia22_At-109
|
Ty1/copia
|
AleII
|
3
|
33
|
| 23
|
Ty1-PROT
|
Wicker_Barbara_A_210J24-3
|
Ty1/copia
|
Maximus/SIRE
|
2
|
31
|
| 24
|
Ty1-PROT
|
ATCOPIA43I
|
Ty1/copia
|
Maximus/SIRE
|
2
|
33
|
| 25
|
Ty1-INT
|
Wicker_Inga_AY661558-2
|
Ty1/copia
|
Maximus/SIRE
|
1
|
40
|
| 26
|
Ty1-INT
|
Wicker_Barbara_A_210J24-3
|
Ty1/copia
|
Maximus/SIRE
|
1
|
39
|
| 27
|
Ty1-INT
|
Llorens_RTvr2_AY900122.1
|
Ty1/copia
|
Tork
|
1
|
31
|
| 28
|
Ty1-GAG
|
Llorens_Araco_AC079131.4
|
Ty1/copia
|
Ivana/Oryco
|
1
|
31
|
| 29
|
Ty1-PROT
|
Wicker_Echidne_Os_cons
|
Ty1/copia
|
Maximus/SIRE
|
1
|
38
|
| 30
|
Ty1-INT
|
ATCOPIA31_I
|
Ty1/copia
|
Ivana/Oryco
|
1
|
33
|
| 31
|
Ty1-INT
|
SHACOP4_I_MT
|
Ty1/copia
|
Ivana/Oryco
|
1
|
33
|
| 32
|
Ty1-PROT
|
Wicker_rn_78-53_Os-102
|
Ty1/copia
|
unclass(Ale)
|
1
|
32
|
| 33
|
Ty1-INT
|
Wicker_Hopscotch_Os-110
|
Ty1/copia
|
AleI/Retrofit
|
1
|
32
|
| 34
|
Ty1-PROT
|
SC-4_I
|
Ty1/copia
|
Ivana/Oryco
|
1
|
31
|
| 35
|
Ty1-INT
|
SC-4_I
|
Ty1/copia
|
Ivana/Oryco
|
1
|
32
|
|
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
|
CL4
|
1227
|
| 2
|
CL12
|
955
|
| 3
|
CL19
|
128
|
| 4
|
CL126
|
2
|
|
reads with similarity to all other neighboring clusters
no mates information available