Comparison of WO-A in w Au and w Mel. Alignment of the WO-A prophage region between wAu and wMel. Matching sequences corresponding to predicted CDSs, identified using ACT and Geneious alignments, are connected by grey blocks. Genes whose sequences differ between strains such that a CDS is not predicted in one strain are not represented in the strain lacking the predicted CDS, but their corresponding sequences are still connected to the CDSs in the other strain by grey blocks. The double-headed black arrow indicate regions that have been drawn inverted relative to their orientation in the genome, for clarity of alignment visualisation. Asterisks indicate genes with differences other than SNPs between wAu and wMel. Internal indels less than 20 bp in size are not shown. Predicted CDSs are colour coded as follows: green, phage structural or replication genes; yellow, conserved hypotheticals; red, hypotheticals; blue, ankyrin repeat genes; magenta, transposases or reverse transcriptases. White arrows indicate sequences that are not annotated in one of the two strains and are probable pseudogenes or mis-annotations. Predicted CDSs that result from interruptions, frameshifts or nonsense mutations, which are combined into a single CDS in the other strain, are coloured the same as the CDS from which they are derived, even though they may also be pseudogenes.