Strainer display. Screen captures of the Strainer program displaying scaffold 29 and read sequences from Ferroplasma type II community data taken from an acid mine drainage community . The image in (A) shows the entire scaffold. Read alignments were determined using BLAST and are indicated with filled light-grey bars and connected to mate pairs by a thin light-grey line. Dark regions within a read indicate where the local divergence from the reference is more than 8%. The black bar at the top surrounded by a red rectangle represents the entire reference sequence (scaffold 29 in this case). The dark grey arrows immediately below indicate gene locations. Reads outlined in yellow have alignments, along with their mate pairs (not visible in this image), that are inconsistent with the size of clones. Clusters of such reads indicate an inconsistency in gene order, usually associated with transposable elements or the insertion and deleting of genes. The image in (B) shows a zoomed-in view of the same data. The red rectangle over the reference sequence bar has shrunk to indicate the location of the zoomed view. The user has selected, via a mouse click, one gene. This gene is colored white with a grey region below to indicate its extent. Reads are now white with colored tick marks where they differ in nucleotide sequence from the reference. As detailed in (C), blue, red, purple, and green ticks indicate substitutions for the bases A, C, T and G respectively. Ticks of half height indicate extra bases in a read sequence, and missing bases are colored black. Light grey ticks indicate low quality differences between the read and reference sequences.