a NUCmer alignments (≥20 Kbp length) between chromosome 6A (chr6A) of the Mace and Stanley assemblies. Each data point represents a single pairwise alignment, with the position corresponding to the midpoint of the alignment with respect to the Mace (x-axis) and Stanley (y-axis) assemblies. b % sequence identity of the pairwise NUCmer alignments between chr6A of Mace and Stanley in (a) with respect to the position in the Mace assembly. Each data point represents a single pairwise alignment. c Close-up view of (b) (red bar) between 99.90 and 100.00 % sequence identity. d Boxplots show the pairwise NUCmer alignments between chr6A of Mace and Stanley from (b) grouped into 5-Mbp bins. Grey-filled boxplots indicate bin median ≥99.99% sequence identity. Pink-shaded regions indicate intervals defined as haplotype blocks using the NUCmer-based approach (adjacent bins with median ≥99.99% stitched together allowing for two bins below the threshold, see “Methods”). e Diagrammatic representation of haplotype blocks between Mace and Stanley on chr6A called in (d). Mace physical position is a common axis for (a–e). f Pairwise BLAST alignments of genes on chromosome 6A in Mace and Stanley based on projections of RefSeqv1.1 high-confidence gene models (ordered by RefSeqv1.1 coordinates). The amount of flanking sequence included is indicated on the left, n indicates number of genes (sequences with Ns were excluded). Black = 100% identity, grey = <100% identity. Numbered boxes/pink rectangles above the heatmaps show the locations of NUCmer-based haplotype blocks defined in (e). Blue boxes below the heatmaps are haplotype blocks called based on BLAST alignments (25-gene sliding window; see “Methods”).