Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories in the directory subtelomere contain instructions and scripts for reproducing many of the results in the manuscript. The subdirectory subtelomere/TwoCopies/ contains two subdirectories of instructions and scripts for reproducing the results in the table on the average coverage of Focb TR4 isolates. The subdirectory subtelomere/TEs/ contains four subdirectories, each of which provides instructions and scripts for estimating the copy numbers of one or two transposons in the table on the copy numbers of five transposons in Focb TR4 isolates. The subdirectory subtelomere/SVs/ explains how the results on SNPs and presence/absence polymorphisms could be reproduced. The subdirectory subtelomere/Fol/ contains three subdirectories, each of which includes information for reproducing one of the three columns in the table on mean SNP rates between Fol D11 and each of Fol4287, Fol069 and Fol072. The subdirectory subtelomere/Forc/ demonstrates how some of the programs and scripts developed by the author are used to analyze a genome assembly of Forc isolate Forc016. The subdirectory subtelomere/pub/ contains the source and executable code of those programs. See the README and z.cmd files in each leaf subdirectory for more information