This track depicts masked sequence as determined by WindowMasker on the the 09 May 2016 Mus musculus (house mouse)/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1 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 GCA_001632555.1_C57BL_6NJ_v1.unmasked.fa -output wm_counts
windowmasker -ustat wm_counts -sdust true -input GCA_001632555.1_C57BL_6NJ_v1.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.bed
The 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 707,466,016 bases in the assembly size 2,806,800,287 for
a percent coverage of % 25.21.
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