Figure 2: Flow of the BES analysis. To eliminate repetitive sequences, 93,682 BESs were initially searched against the repeat dataset of ITAG 2.3 with a BLASTN cutoff value of E <10−50. Next, the remaining sequences were mapped onto the “Heinz 1706” pseudomolecule sequences (SL2.40) under the following criteria: identity >90%, coverage >50%; E <10−100; the inclusion of single hits only. Mapped BESs were classified as either unique pair ends, for which both ends were mapped, or unique ends, for which only one end was mapped.