Table 2 |
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|
Repeat analysis of individual contigs from D. virilis compared to D. melanogaster |
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|
Contig |
Size (bp) |
1360 % |
DINE-1 % |
DNA % |
Retro % |
Simple % |
Unk % |
Total % |
|
|
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|
Drosophila virilis dot chromosome contigs |
||||||||
|
30 |
61,074 |
1.9 |
0.0 |
5.6 |
15.1 |
5.6 |
1.8 |
30.1 |
|
50 |
56,333 |
0.0 |
0.0 |
3.7 |
0.0 |
2.8 |
5.3 |
11.9 |
|
103 |
39,850 |
0.0 |
0.0 |
7.8 |
5.6 |
5.7 |
4.3 |
23.3 |
|
106 |
40,734 |
2.6 |
0.0 |
7.4 |
4.0 |
5.5 |
0.6 |
20.1 |
|
67 |
54,154 |
0.0 |
0.1 |
3.8 |
10.3 |
6.0 |
0.1 |
20.3 |
|
113 |
37,265 |
0.0 |
0.2 |
5.8 |
20.5 |
6.2 |
0.3 |
33.0 |
|
Totals |
289,410 |
0.8 |
0.1 |
5.5 |
9.1 |
5.2 |
2.2 |
22.8 |
|
72 |
43,948 |
0.3 |
0.4 |
9.7 |
1.4 |
10.5 |
1.1 |
23.4 |
|
91 |
39,292 |
0.0 |
0.0 |
0.2 |
9.2 |
6.8 |
0.5 |
16.7 |
|
Drosophila melanogaster dot chromosome contigs |
||||||||
|
30.1 |
40,013 |
2.0 |
6.0 |
0.0 |
3.2 |
6.9 |
0.1 |
18.2 |
|
30.2 |
23,681 |
14.4 |
6.7 |
0.0 |
25.6 |
2.9 |
4.6 |
54.3 |
|
50.1 |
43,617 |
10.0 |
4.2 |
5.4 |
0.0 |
2.4 |
0.0 |
22.0 |
|
50.2 |
34,148 |
4.8 |
9.3 |
12.1 |
4.7 |
2.9 |
0.2 |
34.0 |
|
103 |
40,295 |
5.4 |
14.6 |
6.1 |
0.7 |
2.7 |
0.2 |
29.8 |
|
106 |
38,285 |
0.0 |
21.8 |
0.8 |
3.2 |
2.0 |
0.3 |
28.1 |
|
67 |
44,243 |
0.1 |
8.1 |
4.6 |
0.0 |
3.7 |
0.2 |
16.7 |
|
113 |
36,538 |
0.0 |
13.0 |
0.1 |
6.2 |
2.7 |
0.4 |
22.4 |
|
Totals |
300,820 |
4.1 |
10.5 |
3.8 |
4.2 |
3.3 |
0.5 |
26.5 |
|
Entire 4th |
1,237,870 |
3.8 |
9.2 |
3.0 |
9.5 |
2.9 |
0.0 |
28.4 |
|
Drosophila virilis contigs from major chromosomes |
||||||||
|
13 |
40,479 |
0.0 |
0.0 |
0.4 |
1.0 |
8.6 |
0.3 |
10.3 |
|
112 |
34,783 |
0.0 |
0.0 |
0.0 |
0.7 |
17.8 |
0.0 |
18.6 |
|
121 |
47,154 |
0.0 |
0.0 |
0.0 |
0.0 |
3.4 |
0.0 |
3.4 |
|
122 |
41,111 |
0.0 |
0.0 |
0.6 |
0.1 |
3.1 |
0.0 |
3.8 |
|
Totals |
163,527 |
0.0 |
0.0 |
0.2 |
0.4 |
7.7 |
0.1 |
8.4 |
|
11 |
40,809 |
0.0 |
0.1 |
0.3 |
0.0 |
7.6 |
0.3 |
8.3 |
|
80 |
68,774 |
0.0 |
0.1 |
0.2 |
0.6 |
4.4 |
0.6 |
6.0 |
|
Drosophila melanogaster contigs from major chromosomes |
||||||||
|
13 |
42,664 |
0.0 |
0.0 |
0.0 |
4.1 |
3.7 |
0.0 |
7.8 |
|
112 |
29,021 |
0.0 |
0.2 |
0.0 |
0.0 |
3.7 |
0.0 |
3.9 |
|
121 |
46,784 |
0.0 |
0.0 |
0.0 |
0.0 |
1.1 |
0.0 |
1.1 |
|
122 |
55,801 |
0.0 |
0.0 |
0.0 |
10.6 |
1.6 |
0.0 |
12.2 |
|
Totals |
174,270 |
0.0 |
0.0 |
0.0 |
4.4 |
2.3 |
0.0 |
6.8 |
|
|
||||||||
|
Individual contigs from D. virilis are shown in each row with the homologous region from D. melanogaster shown below. Total size of the contig is shown in bp, followed by percentage of the contig made up of DNA transposons (separated into 1360, DINE-1 and all other DNA transposons), retroelements, simple repeats, and repeats of unknown type (see Materials and methods). Total repeats in the last column is for the contig in that row, and the bold row at the bottom of each group represents the totals for that group. Rows below the bold row represent D. virilis contigs where a homologous region from D. melanogaster could not be defined, so they were not used in the calculations of total repeat density (see Materials and methods). |
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|
Slawson et al. Genome Biology 2006 7:R15 doi:10.1186/gb-2006-7-2-r15 |
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