The output of reputer consists of two-copy repeats that are classed into elements after being clustered together regarding their position in the chromosome and their overlapping with other repeats. CRs are composed of shortly spaced nonoverlapping nontandem repeats. SPIDRs contain multiple nontandem occurrences of repeats, whose spacers show no significant similarity. TRs/SSRs are composed of tandem motifs, which in SSRs are smaller than 6 nt, whereas in TRs they are larger. The elements that cannot be unambiguously classified are grouped as “others.” The repeatability profiles measure the extent of repeatability of each region of the element elsewhere in the element (see Methods).
