Method and apparatus for identifying tandem repeats in a nucleotide sequence

A method of detecting a tandem repeat in a nucleotide sequence, the method comprising:

• constructing a self-alignment plot of a nucleotide sequence;
• identifying one or more candidate alignments present in the self-alignment plot, the identified candidate alignments being represented by lines positioned parallel to a central diagonal line of the self-alignment plot, the central diagonal line indicating alignment of the nucleotide sequence with itself;
• identifying one or more square-shaped subregions (SSS) representing a tandem repeat and each associated with a plurality of identified candidate alignments by:
• i) estimating, for a plurality of the one or more candidate alignments, a defining point of an individual square, each candidate alignment having a start point and an end point, the start point and the end point being positioned along adjacent sides of the individual square;
• ii) selecting one or more seed alignments from the one or more candidate alignments;
• iii) associating the one or more candidate alignments with the one or more seed alignments, the associating comprising clustering defining points of individual squares of the one or more candidate alignments around the defining points of the one or more seed alignments, thereby determining a final SSS representing a tandem repeat;
• and
• reporting presence of the tandem repeat in a region of the nucleotide sequence corresponding to the identified final SSS.