Cluster CL3

Cluster summary

Number.of.reads Number.of.pairs Density
13583 468800 0.0051

Summary of RepeatMasker hits

  class.fammily class family hits hits[%] content Mean_Score
3 LTR/Copia LTR Copia 6990 51.5000 45.2357 335
4 Simple_repeat Simple_repeat Simple_repeat 15 0.1100 0.0438 259
5 Low_complexity Low_complexity Low_complexity 11 0.0810 0.0321 24
6 RC/Helitron RC Helitron 1 0.0074 0.0065 235
7 LTR/Gypsy LTR Gypsy 1 0.0074 0.0047 231

Summary of RepeatMasker custom library hits

  class.fammily class family hits hits[%] content Mean_Score
3 DNA/DCRE2/DCRE2 DNA DCRE2 1189 8.7500 8.0055 653
4 DNA/DCRE15/DCRE15 DNA DCRE15 309 2.2700 1.9396 608
5 DNA/DCRE5/DCRE5 DNA DCRE5 314 2.3100 1.6951 349
6 DNA/DCRE10/DCRE10 DNA DCRE10 202 1.4900 1.1542 315
7 DNA/DCRE21/DCRE21 DNA DCRE21 124 0.9130 0.7416 291
8 DNA/3Mb1 DNA 3Mb1 12 0.0883 0.0364 232
9 DNA/DCRE17/DCRE17 DNA DCRE17 9 0.0663 0.0241 242
10 DNA/DCRE12/DCRE12 DNA DCRE12 2 0.0147 0.0072 282
11 DNA/7Mb1 DNA 7Mb1 1 0.0074 0.0029 279
12 DNA/Plastid_119001-120000 DNA Plastid_119001-120000 1 0.0074 0.0025 290
13 DNA/Plastid_80501-81500 DNA Plastid_80501-81500 1 0.0074 0.0025 295
14 DNA/Plastid_83001-84000 DNA Plastid_83001-84000 1 0.0074 0.0024 276

Summary of TE domain hits

Number of similarity hits for individual sequences
  Domain ID Type Lineage Hits MeanScore
1 Ty1-RT Wicker_Echidne_Os_cons Ty1/copia Maximus/SIRE 491 45
2 Ty1-RT SIRE1_INT_ Ty1/copia Maximus/SIRE 373 48
3 Ty1-INT Wicker_Usier_11O9-1 Ty1/copia Maximus/SIRE 332 40
4 Ty1-RT Wicker_Maximus_cons Ty1/copia Maximus/SIRE 332 51
5 Ty1-RH Wicker_Osr9_Os_cons Ty1/copia Maximus/SIRE 299 47
6 Ty1-INT Wicker_Barbara_A_210J24-3 Ty1/copia Maximus/SIRE 277 45
7 Ty1-RT Wicker_Osr8_Os_cons Ty1/copia Maximus/SIRE 266 44
8 Ty1-INT Wicker_Osr8_Os_cons Ty1/copia Maximus/SIRE 230 41
9 Ty1-RH Wicker_Inga_AY661558-2 Ty1/copia Maximus/SIRE 220 44
10 Ty1-RH Wicker_Barbara_A_210J24-3 Ty1/copia Maximus/SIRE 215 50
11 Ty1-RT Wicker_Osr10_Os_cons Ty1/copia Maximus/SIRE 211 49
12 Ty1-RT ATCOPIA43I Ty1/copia Maximus/SIRE 202 49
13 Ty1-RT Wicker_Osr9_Os_cons Ty1/copia Maximus/SIRE 201 44
14 Ty1-RT Wicker_Usier_11O9-1 Ty1/copia Maximus/SIRE 175 42
15 Ty1-RH Wicker_Echidne_Os_cons Ty1/copia Maximus/SIRE 174 49
16 Ty1-RH Wicker_Osr10_Os_cons Ty1/copia Maximus/SIRE 172 50
17 Ty1-INT Wicker_Inga_AY661558-2 Ty1/copia Maximus/SIRE 149 43
18 Ty1-INT Wicker_Maximus_cons Ty1/copia Maximus/SIRE 107 35
19 Ty1-INT Wicker_Marcus_Os-1 Ty1/copia Maximus/SIRE 94 43
20 Ty1-RT Wicker_Barbara_A_210J24-3 Ty1/copia Maximus/SIRE 94 47
21 Ty1-RH Wicker_Maximus_cons Ty1/copia Maximus/SIRE 83 49
22 Ty1-INT Wicker_ATCopia43_At-1 Ty1/copia Maximus/SIRE 71 48
23 Ty1-RT Wicker_Inga_AY661558-2 Ty1/copia Maximus/SIRE 71 45
24 Ty1-RT COPIA3-I_LC Ty1/copia Maximus/SIRE 69 52
25 Ty1-RH Wicker_Osr8_Os_cons Ty1/copia Maximus/SIRE 68 52
26 Ty1-INT GmCOPIA11_I Ty1/copia Ivana/Oryco 56 33
27 Ty1-RT Wicker_ATCopia58_At-101 Ty1/copia Maximus/SIRE 55 46
28 Ty1-INT Wicker_Echidne_Os_cons Ty1/copia Maximus/SIRE 51 38
29 Ty1-INT Wicker_ATCopia58_At-101 Ty1/copia Maximus/SIRE 50 42
30 Ty1-PROT Wicker_Usier_11O9-1 Ty1/copia Maximus/SIRE 49 34
31 Ty1-INT Wicker_Osr9_Os_cons Ty1/copia Maximus/SIRE 44 44
32 Ty1-RT POPCOP1_I Ty1/copia Ivana/Oryco 40 51
33 Ty1-RT ATCOPIA63_I Ty1/copia Ivana/Oryco 36 53
34 Ty1-RH Wicker_ATCopia58_At-101 Ty1/copia Maximus/SIRE 36 51
35 Ty1-INT TNT1_I Ty1/copia Tork 32 33
36 Ty1-INT Wicker_Osr10_Os_cons Ty1/copia Maximus/SIRE 26 35
37 Ty1-INT Copia-49_ZM-I Ty1/copia Ivana/Oryco 26 32
38 Ty1-RT Copia-54_SB-I Ty1/copia AleI/Retrofit 25 53
39 Ty1-PROT COPIA3-I_LC Ty1/copia Maximus/SIRE 23 33
40 Ty1-INT Wicker_rn_157-332_Os_103 Ty1/copia Ivana/Oryco 19 31
41 Ty1-RT ATCOPIA62_I Ty1/copia AleII 18 39
42 Ty1-PROT Wicker_Maximus_cons Ty1/copia Maximus/SIRE 17 32
43 Ty1-PROT Copia-49_ZM-I Ty1/copia Ivana/Oryco 15 32
44 Ty1-INT SIRE1_INT_ Ty1/copia Maximus/SIRE 15 43
45 Ty1-RT GmCOPIA11_I Ty1/copia Ivana/Oryco 12 52
46 Ty1-INT ATCOPIA31_I Ty1/copia Ivana/Oryco 12 34
47 Ty1-INT Wicker_ATCopia22_At-109 Ty1/copia AleII 11 33
48 Ty1-RH ATCOPIA63_I Ty1/copia Ivana/Oryco 11 56
49 Ty1-INT COPIA3-I_LC Ty1/copia Maximus/SIRE 10 43
50 Ty1-PROT Wicker_Barbara_A_210J24-3 Ty1/copia Maximus/SIRE 10 34
51 Ty1-INT ATCOPIA63_I Ty1/copia Ivana/Oryco 10 33
52 Ty1-INT ATCOPIA10_I Ty1/copia Tork 10 39
53 Ty1-RT Copia-54_ZM-I Ty1/copia Ivana/Oryco 9 51
54 Ty1-RH SIRE1_INT_ Ty1/copia Maximus/SIRE 9 50
55 Ty1-RT Llorens_Vitico1-1_AM465428.1 Ty1/copia Ivana/Oryco 9 40
56 Ty1-INT Wicker_rn_112-64_Os-101 Ty1/copia Ivana/Oryco 8 33
57 Ty1-RH Wicker_Usier_11O9-1 Ty1/copia Maximus/SIRE 7 50
58 Ty1-RH ATCOPIA43I Ty1/copia Maximus/SIRE 6 50
59 Ty1-INT Wicker_HORPIA_AY661558-1 Ty1/copia Ivana/Oryco 6 31
60 Ty1-INT SHACOP4_I_MT Ty1/copia Ivana/Oryco 6 33
61 Ty1-RT ATCOPIA52_I Ty1/copia AleI/Retrofit 6 49
62 Ty1-RT Copia-53_ZM-I Ty1/copia Ivana/Oryco 6 47
63 Ty1-PROT Llorens_Vitico1-2_AM462010.2 Ty1/copia unclass(AleI/Retrofit) 5 34
64 Ty1-PROT Wicker_Osr10_Os_cons Ty1/copia Maximus/SIRE 5 32
65 Ty1-RH COPIA3-I_LC Ty1/copia Maximus/SIRE 5 49
66 Ty1-RT ATCOPIA51_I Ty1/copia AleI/Retrofit 4 50
67 Ty1-RT SHACOP4_I_MT Ty1/copia Ivana/Oryco 3 43
68 Ty1-INT Llorens_Vitico1-2_AM462010.2 Ty1/copia unclass(AleI/Retrofit) 3 32
69 Ty1-INT Copia-53_ZM-I Ty1/copia Ivana/Oryco 2 31
70 Ty1-INT ATCOPIA43I Ty1/copia Maximus/SIRE 2 36
71 Ty1-RT Llorens_Oryco1-1_AL928755.5 Ty1/copia Ivana/Oryco 2 42
72 Ty1-INT COP10_I_MT Ty1/copia AleII 2 31
73 Ty1-RH POPCOP1_I Ty1/copia Ivana/Oryco 2 48
74 Ty1-INT ATCOPIA49_I Ty1/copia Tork 2 38
75 Ty1-INT COP12_I_MT Ty1/copia Ivana/Oryco 2 37
76 Ty1-RH Copia-48_SB-I Ty1/copia Ivana/Oryco 2 36
77 Ty1-INT COPIA3-I_OS Ty1/copia Tork 1 31
78 Ty1-INT SHACOP6_I_MT Ty1/copia AleII 1 34
79 Ty1-INT SHACOP8_I_MT Ty1/copia Ivana/Oryco 1 40
80 Ty1-INT Copia-54_ZM-I Ty1/copia Ivana/Oryco 1 33
81 Ty1-RT Copia-18_SB-I Ty1/copia Angela 1 42
82 Ty1-RT ATCOPIA1I Ty1/copia AleII 1 41
83 Ty1-INT Wicker_rn_374-205_Os-104 Ty1/copia Ivana/Oryco 1 31
84 Ty1-INT Copia26-ZM_I Ty1/copia AleI/Retrofit 1 31
85 Ty1-INT Wicker_rn_228-214_Os_cons Ty1/copia Ivana/Oryco 1 31
86 Ty1-INT Tvv1_I Ty1/copia AleII 1 31
87 Ty1-INT Llorens_Tork4_EU105455.1 Ty1/copia Tork 1 34
88 Ty1-RT Copia-61_SB-I Ty1/copia AleI/Retrofit 1 47
89 Ty1-INT Copia-18_SB-I Ty1/copia Angela 1 36
90 Ty1-RH Wicker_ATCopia43_At-1 Ty1/copia Maximus/SIRE 1 48
91 Ty1-RH Wicker_Marcus_Os-1 Ty1/copia Maximus/SIRE 1 51
92 Ty1-RT Wicker_Retrofit4_Os-101 Ty1/copia AleI/Retrofit 1 47
93 Ty1-RT Wicker_rn_228-214_Os_cons Ty1/copia Ivana/Oryco 1 49
94 Ty1-RT Wicker_Hopscotch_Os-110 Ty1/copia AleI/Retrofit 1 48
95 Ty1-RH Wicker_SC3_Os_cons Ty1/copia Ivana/Oryco 1 38
96 Ty1-PROT ATCOPIA32_I Ty1/copia Tork 1 32
97 Ty1-RT Copia-17_SB-I Ty1/copia AleI/Retrofit 1 55
98 Ty1-INT Copia-29_SB-I Ty1/copia Ivana/Oryco 1 33
99 Ty1-RT Wicker_rn_18-313_Os-101 Ty1/copia Ivana/Oryco 1 34

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 843
2 CL6 629
3 CL38 118
4 CL39 89
5 CL94 9
6 CL56 2


reads with similarity to all other neighboring clusters

no mates information available