detailed comparison of two genomic sequences

 Dotter is a graphical dot-matrix program for detailed comparison of two
 sequences.
 .
  * Every residue in one sequence is compared to every residue in the
    other, and a matrix of scores is calculated.
  * One sequence is plotted on the x-axis and the other on the y-axis.
  * Noise is filtered out so that alignments appear as diagonal lines.
  * Pairwise scores are averaged over a sliding window to make the score
    matrix more intelligible.
  * The averaged score matrix forms a three-dimensional landscape,
    with the two sequences in two dimensions and the height of the
    peaks in the third. This landscape is projected onto two
    dimensions using a grey-scale image - the darker grey of a peak,
    the higher the score is.
  * The contrast and threshold of the grey-scale image can be adjusted
    interactively, without having to recalculate the score matrix.
  * An Alignment Tool is provided to examine the sequence alignment that
    the grey-scale image represents.
  * Known high-scoring pairs can be loaded from a GFF file and overlaid
    onto the plot.
  * Gene models can be loaded from GFF and displayed alongside the
    relevant axis.
  * Compare a sequence against itself to find internal repeats.
  * Find overlaps between multiple sequences by making a dot-plot of all
    sequences versus themselves.
  * Run Dotter in batch mode to create large, time-consuming dot-plots as
    a background process.