Alignment of five supercontigs containing the longest putative Numts with the mitochondrial genome. On the mitochondrial genome tRNA and rRNA genes are represented by red colour blocks and blocks of other colour indicate the coding genes as named. Corresponding coloured blocks on the supercontigs indicate regions of high homology with the mtDNA with mutational differences indicated below each gene as follows: Line 1 = numbers of synonymous + non-synonymous mutations, Line 2 = number of indels (length of indels in bp), * = Stop codons. Grey-shaded areas indicate regions of no homology and dotted lines represent the rest of the genomic supercontigs. The core haplotypes in clade 2 and clade 1 are identical to the corresponding ND4 regions on supercontigs 1.363 and 1.593, and supercontig 1.1330, respectively.