Obtain satellite DNA monomer from dot plot

Question

[kirillkirilenko]

I have come across numerous articles in which researchers extract monomers of satellite DNA, creating dot plots from contigs that contain this satellite. For instance, in the article linked doi: 10.3390/ijms22116052 the process is described as follows: 'For each candidate cluster, we selected the longest and highest coverage contig assembled by RepeatExplorer2 to generate a dot plot using the Dotmatcher tool. Subsequently, contigs were separated into monomers to align them using MAFFT and generate a consensus sequence.'

I can create a dot plot, and I observe numerous matching lines off the main diagonal, indicating repeats. However, I am uncertain about how to separate contig into monomers. Are the monomers comprised of all the matching lines, or are they specifically defined by a certain length?

My dot plot:

Answer 1

[shelkmike]

Here, the monomer length is approximately 50 bp. You can determine the consensus sequence of the monomers by TRF (https://tandem.bu.edu/trf/submit_options).
If you need to find all locations of the monomer, I think a suitable method is to align the consensus sequence to the entire region using BLASTN or PSI-BLAST.