Gene order differences. Illustrations of gene order differences appearing in Strainer. Reads from Leptospirillum group II were assembled into contigs by Phred/Phrap. One contig and its component reads were imported from the Phrap generated ACE file and are shown in (A). Reads with gene orders that do not match the reference sequence stand out due to high levels of differences. Panel (B) shows a segment of the same region at higher zoom revealing similar patterns in all the differing reads. In (C), reads from Ferroplasma type I were aligned against the Ferroplasma acidarmanus isolate genome using blastn. BLAST cuts off alignments when the similarity ends, but gene order differences are still apparent due to multiple reads being clipped (in blue) at the same point and a cluster of reads (in yellow) missing mate-pairs. Panel (D) shows the same region at higher zoom revealing the exact point at which the read alignments are trimmed.