  <SECT2 ID="DISPLAYMENU-GC-CONTENT">
    <TITLE>GC Content (%)</TITLE>
    <PARA>
Controls whether the GC content plot is visible.  This is a graph of the
average GC content of a moving window (default size 120 base), across the
bases visible in the overview window.
[Default: off] [short name: <LITERAL>gc_content</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-GCSD-CONTENT">
    <TITLE>GC Content (%) With 2.5 SD Cutoff</TITLE>
    <PARA>
Controls whether the cutoff GC content plot is visible.  This is similar to
the GC content graph, but the plot is clipped so that the GC content of each
algorithm window is shown only when it is more than 2.5 times the standard
deviation of the GC content in all the windows.
[Default: off] [short name: <LITERAL>sd_gc_content</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-AG-CONTENT">
    <TITLE>AG Content (%)</TITLE>
    <PARA>
Controls whether the AG content plot is visible.  This is a graph of the
average AG content of a moving window (default size 120 base), across the
bases visible in the overview window.
[Default: off] [short name: <LITERAL>ag_content</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-GC-FRAME-PLOT">
    <TITLE>GC Frame Plot</TITLE>
    <PARA>
Controls whether the GC frame plot is visible.  This graph is similar to the
GC content graph but shows the GC content of the first, second and third
position independently.  For more information on the algorithm and on how to
interpret the result see <ULINK
URL="http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl" TYPE="external">this web
page</ULINK>.
[Default: off] [short name: <LITERAL>gc_frame</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-CORRELATION-SCORES">
    <TITLE>Correlation Scores</TITLE>
    <PARA>
Controls whether the (forward) correlation scores plot is visible.  The graph
shows the correlation between the amino acid composition of the globular
proteins in TREMBL and the composition of the base translation in each of the
three reading frames.  The green line represents forward frame 1, blue
represents frame 2 and red represents frame 3.
[Default: off] [short name: <LITERAL>correlation_score</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-REVERSE-CORRELATION-SCORES">
    <TITLE>Reverse Correlation Scores</TITLE>
    <PARA>
This does the same as "Correlation Scores", but does the calculation on the
reverse strand.  The green line represents reverse frame 1 (the bottom frame
line), blue represents frame 2 and red represents frame 3.
[Default: off] [short name: <LITERAL>correlation_score</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-GC-DEVIATION">
    <TITLE>GC Deviation (G-C)/(G+C)</TITLE>
    <PARA>
Controls whether the GC deviation plot is visible.  This graph shows the
difference between the "G" content of the forward strand and the reverse
strand.
[Default: off] [short name: <LITERAL>gc_deviation</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-AT-DEVIATION">
    <TITLE>AT Deviation (A-T)/(A+T)</TITLE>
    <PARA>
Controls whether the AT deviation plot is visible.  This graph shows the
difference between the "A" content of the forward strand and the reverse
strand.
[Default: off] [short name: <LITERAL>at_deviation</LITERAL>]
    </PARA>
  </SECT2>
