Table 2.
Sequence composition of genome-wide 454 reads and of the sequences adjacent to pSc200 and pSc250 arrays
| All reads | Reads with junctions of pSc200 | Reads with junctions of pSc250 | ||||
|---|---|---|---|---|---|---|
| Type of sequence | Cumulative length, bp | Proportion to cumulative length, % | Cumulative length of non-tandem DNA, bp | Proportion, % | Cumulative length of non-tandem DNA, bp | Proportion, % |
| Class I TE | ||||||
| Ty3/Gypsy-like | 4 142 315 628 | 50.84 | 36542 | 35.68 | 65786 | 40.62 |
| Ty1/Copia-like | 799 492 074 | 9.81 | 14322 | 13.99 | 14677 | 9.06 |
| solo-LTR | 60 362 185 | 0.74 | 13119 | 12.81 | 37289 | 23.02 |
| LINE | 57 651 280 | 0.71 | 483 | 0.47 | 1212 | 0.75 |
| SINE | 1 201 224 | 0.02 | 0 | 0.00 | 0 | 0.00 |
| Class II TE | ||||||
| CACTA | 454679975 | 5.58 | 5544 | 5.41 | 5621 | 3.47 |
| EnSpm | 18661838 | 0.23 | 984 | 0.96 | 23 | 0.01 |
| Harbinger | 20519563 | 0.25 | 0 | 0.00 | 0 | 0.00 |
| Mariner | 24069442 | 0.30 | 370 | 0.36 | 147 | 0.09 |
| Hat | 12376913 | 0.15 | 0 | 0.00 | 268 | 0.17 |
| Helitron | 3779908 | 0.05 | 0 | 0.00 | 0 | 0.00 |
| Others | 37550591 | 0.46 | 124 | 0.12 | 307 | 0.19 |
| Simple repeats, low complexity | 27 883 202 | 0.34 | 259 | 0.25 | 383 | 0.24 |
| rDNA | 8 782 174 | 0.11 | 0 | 0.00 | 396 | 0.24 |
| Tandem repeats | 16 953 966 | 0.21 | 185 | 0.18 | 2420 | 1.49 |
| Unclassified (unknown) | 48 627 218 | 0.60 | 2348 | 2.29 | 2996 | 1.85 |
We computed DNA composition of all reads and compared with that in non-tandem DNA adjacent to the pSc200 and pSc250 tandem arrays. Length of all repeats was defined according to annotations that we got in output files of RepeatMasker tool (see “Methods”). Columns “Proportion” denote the ration of the cumulative length of the given non-tandem DNA to the cumulative length of all reads