====== Sequence View ======
  * The sequence view allows you to see the details of the design sequence.
===== The Sequence Navigation Windows =====
    * There are two movable windows to allow navigation through through the sequence:
=== The Global Sequence Window ===

      * The global sequence window (label in screenshot 3) allows selection of a large area of the construct
        * In a circular construct, the global window can straddle the origin.
        * The size of the global window can be altered by dragging one of the open squares at its boundary (label in screenshot 3).
        * The location of the global window can be altered by: 
          * clicking anywhere within the selected part of the sector and dragging it.
          * clicking anywhere on the construct: the click point will become the center of the window.

=== The Local Sequence Window ===
      * The local sequence window (label in screenshot 3) allows base-by-base navigation through the sequence
        * The local window can be moved in the same way as the global window.
        * The sequence within the local window is displayed (label in screenshot 3).
{{:ui:sequence_view2.jpg}}
===== The Sequence Display =====
  * At the top of the sequence display, the sequence of the final construct is shown.
     * Below the construct sequence is a grid where [[guide:create oligonucleotides | oligonucleotides]] are created and displayed.
     * Below the oligonucleotide grid, the sequence of each element is displayed in a sequence bar.  Above the sequence bar is the name for that element and an arrow denoting its orienation.
     * The sequences for DNA elements and amino acid elements are displayed differently:

=== Display of Amino Acid element sequence ===
  * The amino acid sequence bar shows the amino acid sequence of the element
     * Beneath each amino acid, each of the codons encoding that amino acid are displayed
       * The codons are shown in the order of their frequencies in the codon table selected for the construct
         * The highest frequency codon is at the top
       * The codon that is currently selected to encode each amino acid is colored
         * Codons whose frequencies are higher than the threshold frequency are colored green.
         * Codons whose frequencies are lower than the threshold frequency are colored yellow.
           * The threshold frequency can be changed in the [[ui:Details View]]
       * A new codon may be selected to encode any amino acid by clicking on a different codon button.
           * The new choice changes the sequence displayed for the final construct.
           * The new choice changes the sequence of any oligonucleotide that overlaps the change.
           * Clicking on the codon that is already selected will clear that codon choice and leave a gap in the final construct sequence.
       * For amino acid elements that are in the reverse direction, the codons are shown in the forward direction beneath the amino acid
          * underneath a methionine in a reverse direction amino acid element the codon is displayed as ATG
          * the sequence of the final construct above the methionine is shown correctly as CAT
{{:ui:sequence_view3.jpg}}
=== Display of DNA element sequence ===
  * The DNA sequence bar shows the DNA sequence of the element
     * Beneath each triplet, each encoded amino acid is displayed
       * There are 6 different amino acid sequences shown, 3 in the forward reading frames and 3 in the reverse.
         * The amino acid one letter code is shown in line with the middle nucleotide of the codon.
         * The direction of the reading frame is indicated by a faint arrow. 
       * If a DNA element is adjacent to an amino acid element, the reading frame that is in the same frame as the amino acid element will be colored to match that element.


===== Editing Sequence Elements within the Sequence View =====
  * The sequence of individual elements within the final construct can be [[guide:edit | edited]] in the Sequence View.