Additional file 2 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species

Additional file 2: Table S1. Sequences used for Fig. 5. The scheme is based on the sequences and description in corresponding references. Table S2. Evaluation of G-forming potential of telomeric LINE elements. Table S3. Sequences of D. melanogaster Jockey elements used for construction of Fig. 2D. Table S4. Sequences used for RT based phylogeneitc tree construction in Figure S4A. Table S5. Sequences used for GAG based phylogeneitc tree construction in Figure S4A. Table S6. RT domains used for construction of Figure S12. Table S7. Telomeric and potential telomeric scaffolds used for PQS density assesment (Figure S5). All Ns were removed from the analysis but are included in used regions. All regions that we could not indentify faithfully as telomeric elements were removed from analysis and are not included in used regions. Table S8. Sequences used for visualisation of telomeric and potential telomeric scaffolds in Fig. 3. The "Start & Stop" postions correspond to visualized regions. Table S9. GAG DNA and AA sequences used for Fig. 4. Conserved domain coresponds to bp 1402–2055 and AA 468–685 in Dmel_HetA. Table S10. Pol (RT) DNA and AA sequences used for Fig. 4. Table S11. Sequences used for Figure S7. Aminoacid sequences can be obtained by simple translation of these sequences. Table S12. DNA and AA identity and similarity, including dn/ds ratios.

附加文件2：表S1。用于图5的序列。本研究方案基于相关参考文献中的序列与描述内容构建。表S2。端粒LINE元件（telomeric LINE elements）的G-四链体形成潜力评估。表S3。用于构建图2D的黑腹果蝇（D. melanogaster）Jockey元件序列。表S4。用于图S4A中基于逆转录酶（RT）的系统发育树构建的序列。表S5。用于图S4A中基于GAG蛋白的系统发育树构建的序列。表S6。用于构建图S12的逆转录酶结构域序列。表S7。用于平行G四链体序列（PQS）密度评估（图S5）的端粒及潜在端粒支架序列。所有含N碱基的序列均未纳入分析，但已被计入所用区域范围。所有无法被准确鉴定为端粒元件的区域均已从分析中剔除，未纳入所用区域。表S8。用于图3中端粒及潜在端粒支架可视化的序列。其中的"Start & Stop"位置对应可视化区域。表S9。用于图4的GAG蛋白DNA及氨基酸（AA）序列。其保守结构域对应Dmel_HetA中碱基对1402–2055及氨基酸468–685的区域。表S10。用于图4的Pol（逆转录酶RT）DNA及氨基酸序列。表S11。用于图S7的序列。通过对这些序列进行简单翻译即可获得对应的氨基酸序列。表S12。DNA与氨基酸（AA）的同源性、相似性分析结果，包括dn/ds比值。