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      "\n",
      "k-mer-based analysis of the oyster genome showed that ~35% of 17-mers had at least two identical copies in the genome, suggesting an abundance of repetitive sequences (Supplementary Fig. 1). Similarly, homology searching and ab initio prediction found 202\u2009Mb (36% of the genome) in repetitive sequences (Supplementary Text C2 and Supplementary Table 8). Over 62% of the detected repeats could not be assigned to known categories, reflecting the paucity of genomic information from molluscs22. Large numbers of transposase (359) and reverse-transcriptase (779) gene fragments were detected; over 96% of these had detectable transcripts (Supplementary Fig. 8). Alignment of the wild sequence against the assembly identified 20,605 deletions (>100\u2009bp), over 80% of which overlapped with detected transposable elements, suggesting that transposable elements may have an active role in shaping genome variation. Using MITE-hunter23, we detected 157,007 copies of miniature inverted-repeat transposable elements (MITEs), accounting for a remarkable 8.82% of the genome (Supplementary Text C2.3 and Supplementary Table 9). Pair-wise comparisons show extremely low sequence divergence in some MITE families (Supplementary Fig. 9), indicating that they may still be active.\n"
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