Additional file 1:

Alignment of the sequenced GlaI, Sse9I and AspS9I fragments. Numbering is given according to consensus sequence [11]. ACGT sites are given with yellow background. Nucleotides which differ from those in consensus are given with blue background. Sse9I fragments (names start with S) and AspS9I fragments (names start with A) are indicated in green. Some pieces of fragments (shown in magenta) were moved in the alignment to fit to a total length of 234 bp. CG dinucleotides are shown in blue. Yellow background indicates ACGT sites (cleaved or not cleaved).

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Additional file 2:

Alignment of 30 γ-satellite MnlI DNA fragments (Vissell and Choo, [13]). Numbering is given according to consensus sequence [11]. ACGT sites are given with yellow background. CG dinucleotides are in blue. Consensus sequence obtained from this alignment is given at the bottom (grey background) and positions which differ from those in a known consensus [11] are indicated by blue background.

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Additional file 3:

Alignment of 140 γ-satellite DNA monomers from chromosome 9. Explanations are the same as for Additional file 2.

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Additional file 4:

Alignment of 40 γ-satellite DNA fragments from chromosome 3. Explanations are the same as for Additional file 2.

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