To create figures, run the R code

1. *00_General.R* to load basic objects and functions. Before running the code, `setwd()` must be used to define working directory.
2. *01_CreateFigures.R* to create individual figures for main text or supplementary data

---

**List of created figures:**

Main text figures
- **Figure 1** - Sequence logos of retroviral PPM0s (whole IS set) and palindromic defect (PDef).
- **Figure 2** - whole mixture M08 for selected IS sets
- **Figure 3** - nucleotide combinations - legend of created figure is modified and is not identical to the legend in the paper
- **Figure 4** - HIV-1 intra-Alu hotspot

Supplementary figures (Supplementary to figure ...)
- **Figure S1** (Figure1) - PDef
- **Figure S2** (Figure2) - whole mixtures M02-M08 - separate figures for each "M"s are created, stored in separated folder and later joined to single pdf
- **Figure S3** (Figure3A) - nucleotide combinations - KLID
- **Figure S4** (Figure3B) - nucleotide combinations - Frequencies
- **Figure S5** (Figure3D) - nucleotide combinations - Most-Least Freq
- **Figure S6** (Figure4H) - Alu_Motif_Dist_All
- **Figure S7** (Figure4I) - Alu_Motif_Freq_All
- **Figure S8** - comparision of ASLV IS data set and presentation of the suspicious results regarding alpha_Moiani IS set

