====== Sequence Motif Search ======
(link to screenshot 10)
GeneDesigner permits you to search for any sequence that exists within a construct.
 

===== Searching for a DNA sequence or sequence motif within a construct =====
In [[ui:Sequence View]] select the "Find" panel (label in screenshot 9)
  * Select the "Motifs" tab
  * Select a [[guide: managed lists | motif]] from the list, or type a sequence into the "Sequence" box
    * Use IUPAC standard bases to define degeneracies
    * Use {x,y} to permit flexibility within the definitions
      * For example ARGARGN{3,10}VTG = A[A/G]GA[A/G]G followed by between 3 and 10 bases then CTG, GTG or ATG
  * Click the "Find" button
    * Results are displayed in a hit list, which displays the position of each sequence or motif found
    * Clicking on the sequence / motif in the hit list highlights the site within the [[ui:Sequence View | local sequence window]]
  * Initiate a new search by clicking on the "back/clear" button

=== Restricting your search ===
  * The default settings are to search for the selected sequence / motif within every construct in the project
  * To limit the search to a single construct, or just a part of a construct, select the "Restrict Search" button (label in screenshot 9).
    * Selecting this button will restrict the search to constructs or elements that are highlighted in the [[ui:navigation_pane | Navigation Pane]].