Fig. 1.

Architecture of cenX. centroFlye assembly of cenX consists of over 1510 HORs that represent units of centromeric ETRs. Five HORs are colored by five shades of blue illustrating HOR variations. Each HORs is a nested tandem repeat formed by various monomers of length $171$ bp. The vast majority of HORs on cenX, referred to as canonical HORs, are formed by 12 monomers (shown by 12 different colors). Figure on top represents the dot plot of a canonical HOR that reveals 12 monomers (also known as alpha satellites). While HORs are 95–100% similar, monomers are only 65–88% similar. In addition to the canonical 12-monomer HORs, there is a small number of non-canonical HORs with varying numbers of monomers. Given a read sampled from a centromere and a set of monomers (referred to as blocks in the String Decomposition Problem), SD translates the read into a monoread written in the monomer alphabet