Cluster CL4

Cluster summary

Number.of.reads Number.of.pairs Density
10152 548078 0.011

Summary of RepeatMasker hits

  class.fammily class family hits hits[%] content Mean_Score
3 LTR/Copia LTR Copia 5217 51.4000 45.7863 333
4 Low_complexity Low_complexity Low_complexity 341 3.3600 1.6366 28
5 DNA/hAT-Tag1 DNA hAT-Tag1 1 0.0098 0.0077 226
6 DNA/PIF-Harbinger DNA PIF-Harbinger 1 0.0098 0.0070 249
7 Simple_repeat Simple_repeat Simple_repeat 1 0.0098 0.0024 207

Summary of RepeatMasker custom library hits

  class.fammily class family hits hits[%] content Mean_Score
3 DNA/DCRE10/DCRE10 DNA DCRE10 2219 21.9000 20.1329 664
4 DNA/DCRE5/DCRE5 DNA DCRE5 255 2.5100 2.2942 734
5 DNA/DCRE21/DCRE21 DNA DCRE21 288 2.8400 2.2618 556
6 DNA/DCRE18/DCRE18 DNA DCRE18 193 1.9000 1.4729 275
7 DNA/7Mb1 DNA 7Mb1 1 0.0098 0.0051 230
8 DNA/Mitochondrion_162001-163000 DNA Mitochondrion_162001-163000 1 0.0098 0.0047 226
9 DNA/Plastid_128001-129000 DNA Plastid_128001-129000 1 0.0098 0.0036 248
10 DNA/Plastid_23001-24000 DNA Plastid_23001-24000 1 0.0098 0.0036 233
11 DNA/DCRE14/DCRE14 DNA DCRE14 1 0.0098 0.0035 261
12 DNA/Mitochondrion_145001-146000 DNA Mitochondrion_145001-146000 1 0.0098 0.0032 229
13 DNA/Plastid_66001-67000 DNA Plastid_66001-67000 1 0.0098 0.0026 228

Summary of TE domain hits

Number of similarity hits for individual sequences
  Domain ID Type Lineage Hits MeanScore
1 Ty1-INT Wicker_Inga_AY661558-2 Ty1/copia Maximus/SIRE 382 46
2 Ty1-RT SIRE1_INT_ Ty1/copia Maximus/SIRE 338 45
3 Ty1-RH Wicker_Osr9_Os_cons Ty1/copia Maximus/SIRE 326 51
4 Ty1-RT Wicker_Osr9_Os_cons Ty1/copia Maximus/SIRE 322 45
5 Ty1-RT Wicker_Usier_11O9-1 Ty1/copia Maximus/SIRE 320 43
6 Ty1-RT Wicker_Maximus_cons Ty1/copia Maximus/SIRE 290 48
7 Ty1-INT Wicker_Usier_11O9-1 Ty1/copia Maximus/SIRE 286 39
8 Ty1-RH Wicker_Barbara_A_210J24-3 Ty1/copia Maximus/SIRE 220 51
9 Ty1-RH Wicker_Inga_AY661558-2 Ty1/copia Maximus/SIRE 216 44
10 Ty1-RT Wicker_Osr8_Os_cons Ty1/copia Maximus/SIRE 214 44
11 Ty1-RT Wicker_Inga_AY661558-2 Ty1/copia Maximus/SIRE 211 49
12 Ty1-RH Wicker_Osr8_Os_cons Ty1/copia Maximus/SIRE 187 51
13 Ty1-RT Wicker_Echidne_Os_cons Ty1/copia Maximus/SIRE 185 41
14 Ty1-RT Wicker_Osr10_Os_cons Ty1/copia Maximus/SIRE 130 41
15 Ty1-RT Wicker_Barbara_A_210J24-3 Ty1/copia Maximus/SIRE 113 46
16 Ty1-INT Wicker_ATCopia43_At-1 Ty1/copia Maximus/SIRE 112 43
17 Ty1-RH Wicker_Osr10_Os_cons Ty1/copia Maximus/SIRE 111 45
18 Ty1-RT Wicker_ATCopia58_At-101 Ty1/copia Maximus/SIRE 76 45
19 Ty1-RH Wicker_Maximus_cons Ty1/copia Maximus/SIRE 71 51
20 Ty1-RT ATCOPIA43I Ty1/copia Maximus/SIRE 58 42
21 Ty1-INT COPIA3-I_OS Ty1/copia Tork 58 34
22 Ty1-INT Wicker_Osr10_Os_cons Ty1/copia Maximus/SIRE 43 33
23 Ty1-RT GmCOPIA11_I Ty1/copia Ivana/Oryco 41 48
24 Ty1-INT Wicker_ATCopia58_At-101 Ty1/copia Maximus/SIRE 38 45
25 Ty1-INT Wicker_Barbara_A_210J24-3 Ty1/copia Maximus/SIRE 33 41
26 Ty1-RH Wicker_Echidne_Os_cons Ty1/copia Maximus/SIRE 33 40
27 Ty1-RT Wicker_Marcus_Os-1 Ty1/copia Maximus/SIRE 33 35
28 Ty1-RT COPIA3-I_LC Ty1/copia Maximus/SIRE 30 44
29 Ty1-RT ATCOPIA63_I Ty1/copia Ivana/Oryco 25 52
30 Ty1-INT Wicker_Maximus_cons Ty1/copia Maximus/SIRE 16 33
31 Ty1-RT Copia-54_ZM-I Ty1/copia Ivana/Oryco 16 49
32 Ty1-RH ATCOPIA43I Ty1/copia Maximus/SIRE 13 55
33 Ty1-RT Llorens_Poco_AC210386.1 Ty1/copia Ivana/Oryco 12 42
34 Ty1-RH Wicker_Inav_AY013246-1 Ty1/copia AleI/Retrofit 11 38
35 Ty1-RT Copia-29_SB-I Ty1/copia Ivana/Oryco 11 49
36 Ty1-INT COPIA3-I_LC Ty1/copia Maximus/SIRE 10 33
37 Ty1-INT Wicker_Osr8_Os_cons Ty1/copia Maximus/SIRE 9 39
38 Ty1-RT Llorens_Araco_AC079131.4 Ty1/copia Ivana/Oryco 8 51
39 Ty1-INT SHACOP4_I_MT Ty1/copia Ivana/Oryco 8 34
40 Ty1-RH Wicker_Usier_11O9-1 Ty1/copia Maximus/SIRE 5 51
41 Ty1-INT ATCOPIA22I Ty1/copia AleII 5 32
42 Ty1-RH SIRE1_INT_ Ty1/copia Maximus/SIRE 3 39
43 Ty1-INT Copia-8_SB-I Ty1/copia AleII 2 32
44 Ty1-RT COP12_I_MT Ty1/copia Ivana/Oryco 2 36
45 Ty1-RT HOPSCOTCH_ZM-I Ty1/copia AleI/Retrofit 2 40
46 Ty1-RT ATCOPIA47_I Ty1/copia AleI/Retrofit 2 42
47 Ty1-INT Copia4-ZM_I Ty1/copia Ivana/Oryco 2 45
48 Ty1-RH Wicker_Kasia_102J11-1 Ty1/copia Ivana/Oryco 2 39
49 Ty1-RT Wicker_Ikeros_A_102J11-1 Ty1/copia Angela 1 44
50 Ty1-INT Wicker_Marcus_Os-1 Ty1/copia Maximus/SIRE 1 45
51 Ty1-INT SIRE1_INT_ Ty1/copia Maximus/SIRE 1 35
52 Ty1-INT Wicker_ATCopia26_At-103 Ty1/copia AleII 1 30
53 Ty1-INT SHACOP6_I_MT Ty1/copia AleII 1 41
54 Ty1-RT Copia-26_SB-I Ty1/copia AleI/Retrofit 1 38
55 Ty1-RT ATCOPIA51_I Ty1/copia AleI/Retrofit 1 48
56 Ty1-INT Wicker_Ostonor1_Os_cons Ty1/copia Angela 1 35
57 Ty1-INT Wicker_HORPIA_AY661558-1 Ty1/copia Ivana/Oryco 1 32
58 Ty1-INT Wicker_Alina_At-1 Ty1/copia AleII 1 31
59 Ty1-RT ATCOPIA1I Ty1/copia AleII 1 34
60 Ty1-RT Llorens_Oryco1-1_AL928755.5 Ty1/copia Ivana/Oryco 1 48
61 Ty1-INT Wicker_Echidne_Os_cons Ty1/copia Maximus/SIRE 1 50
62 Ty1-RH ATCOPIA63_I Ty1/copia Ivana/Oryco 1 45
63 Ty1-INT Wicker_Betsy_Os_cons Ty1/copia AleII 1 30
64 Ty1-INT COP10_I_MT Ty1/copia AleII 1 34
65 Ty1-INT Copia26-ZM_I Ty1/copia AleI/Retrofit 1 34
66 Ty1-RH Copia4-ZM_I Ty1/copia Ivana/Oryco 1 34
67 Ty1-RT Copia27-PTR_I Ty1/copia Ivana/Oryco 1 32
68 Ty1-INT Copia-20_SB-I Ty1/copia Ivana/Oryco 1 45
69 Ty1-RH Wicker_ATCopia43_At-1 Ty1/copia Maximus/SIRE 1 41
70 Ty1-INT COPI2_I Ty1/copia Tork 1 34
71 Ty1-RH Wicker_Marcus_Os-1 Ty1/copia Maximus/SIRE 1 54
72 Ty1-INT CPSC4A_I Ty1/copia Ivana/Oryco 1 43
73 Ty1-RT Wicker_Kasia_102J11-1 Ty1/copia Ivana/Oryco 1 44

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 CL9 1227
2 CL3 843
3 CL5 11
4 CL20 2
5 CL221 1
6 CL98 1


reads with similarity to all other neighboring clusters

no mates information available