This track depicts masked sequence as determined by WindowMasker on the the 11 May 2011 Arabidopsis thaliana/GCF_000001735.3_TAIR10/GCF_000001735.3 genome assembly. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site.
To create this track, WindowMasker was run with the following parameters:
windowmasker -mk_counts true -input GCF_000001735.3_TAIR10.unmasked.fa -output wm_counts windowmasker -ustat wm_counts -sdust true -input GCF_000001735.3_TAIR10.unmasked.fa -output windowmasker.intervals perl -wpe 'if (s/^>lcl\|(.*)\n$//) { $chr = $1; } \ if (/^(\d+) - (\d+)/) { \ $s=$1; $e=$2+1; s/(\d+) - (\d+)/$chr\t$s\t$e/; }' windowmasker.intervals > windowmasker.sdust.bedThe windowmasker.sdust.bed included masking for areas of the assembly that are gap. The file was 'cleaned' to remove those areas of masking in gaps, leaving only the sequence masking. The final result covers 27,089,877 bases in the assembly size 119,667,750 for a percent coverage of % 22.64.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941