Table 1.
REPuter [35] was used to locate and count both forward and inverted repeats in the C. lanceolata chloroplast genome. The minimal repeat size was set to 30 bp and the identity of repeats was set to ≥90%. Fifty-one repeats were detected in the Cunninghamia lanceolata chloroplast genome. Most of them are between 10 and 29 bp in length. Repeats longer than 30 bp are listed in the table.
| Repeat Number | Size (bp) | Repeat Unit | Location |
|---|---|---|---|
| 1 | 30 | AAAAAAGAAAAAATCAACACGAGCAGTAAAA(×2) 1 | rpoC2 (CDS 2) |
| 2 | 36 | TTGGACGATTTAGAATACGAAACTACATTGGACAAT(×2) | ycf2 (CDS) |
| 3 | 132 | AAGTATTATTTTCAATGGAAAAAAGCATTCAAAAGATACTATATTGAATTCATAAAAACATTGAATAAGTATTATTTTGAATGGAAAAAAGTATTATTTTGATTCTGTATTAAATTCATAAAAACATTGAAT(×2) | ycf2 (CDS) |
| 4 | 66 | AAGTATTATTTTGAATGGAAAAAAGTATTAAAAGATTCTGTATTGAATTCATAAAAACATTGAAT(×4) | ycf2 (CDS) |
| 5 | 94 | TTACGAGCAATAATGAAACAAAACTTGCCAAATACAATGATGACATTATATAATGATACATAGAGATATTGTGTTGCGTTGTTTACAAAACATG(×2) | IGS 3 (rpl20, ycf1) |
| 6 | 104 | CAAAACTTGCCAAATACAATGATGACATTATATAATGATACATAGAGATATTGTGTTGCGTTGTTTACAAAACATGTTACGAGCAATAATGAAACAAAACTTGT(×2) | IGS (rpl20, ycf1) |
| 7 | 119 | ACAAAACTTGACAAAACTTGCCAAATACAATGATGACATTCTATAATGATAAATAGAGATATTGTGTTGCGTTGTTTAAATGTTACGAGCAATAATGAAACAAAACTTGTCAAAACTG(×2) | IGS (rpl20, ycf1) |
| 8 | 185 | GGAAAAACAAAAAGAACAAATTGAAAGAATAAGATGCTTAAAATTGACTAATAATATTTTTTTTAATGCAACAAAAATTATTTTAAATACCACTACCACAGGAGGGATATGATCACCACTTTTGCATTGTCTTGGCTACAAAGATGTAGCCCAATAATATTGTTTGGTTTCTATTATGGTTTTTT(×2) | IGS (rpl20, ycf1), ycf1 (CDS) |
| 9 | 30 | GAAAAGAAAAGAGAAAAGAACAAGAAGCAT | ycf1 (CDS) |
| 10 | 66 | ATGAATGAGGCAAAGGATACAAAAATAGACTCCATAACTTCGTCTCAAATGGACTCTTTTTGTAGC(×2) | ycf1 (CDS) |
| 11 | 44 | TTATTATCTCTTCTAAAATTATTTTGAAAGATCTGATTCAATGG(×2) | ycf1, IGS (ycf1, tmp) |
| 12 | 44 | CTCTTCTAAAATTATTTTGAAAGATCTGATTCAATGGTTATAAC(×2) | ycf1, IGS (ycf1, tmp) |
| 13 | 33 | TTTGTTTCAATATTTTCAGAATCTTTGTTTTCC(×3) | accD (CDS) |
1 Parenthetical information refers to repeat numbers. For example, (×2) indicates the number of the repeat unit is 2; 2 CDS = coding sequence; 3 IGS = intergenic spacer.