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The window size for the promoter and TU analyses was 100 bp with a step size of 20 bp.
FST values were calculated for sliding windows of 100 bp with a step size of 25 bp, using popoolation2 [ 28].
The window size was set to 500 bp with a step of 250 bp for all of the analyses.
The window size for the Ka/Ks sliding window plots was 50 bp with a step size of 10 bp.
We aligned the pair of sequences in a window of 57 bp with a step of 3 bp forward.
For calculation of differentially methylated regions (DMRs), M values were analyzed in a sliding window of 1200 bp, with a step of one probe.
Similar(51)
This resulted in alignments with a maximum length of 200 bps (longer alignments were split into overlapping windows of 120 bps with a step size of 40) and a minimum number of aligned sequences (>50% identity) from at least 4 different species.
We then processed the genome in 500 bp windows with a step size of 250 bp searching for fragments with more than 3 hits/500 bp in the female genome and less than one for the male genome.
First, each identified RDNP was divided into 160 bp regions with a step of 10 bp.
Repeat density was calculated using a sliding window of 1 kb with a step size of 500 bp.
We used a Markov order of 3 with a 96 bp window sliding with a step size of 12 bp along the genome.
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