By default, the search tools are hidden. To display them, use Edit > Find or click on the Search alignment tool () in the upper right of the Alignment or Strategy view. This causes the search tools to be displayed on the top left of that view. Different views have different types of search targets. The Alignment view lets you search by all variables in the table below, while the Strategy view only allows you to search for coverage and reference features.

  1. Use the Find drop-down menu to choose the item to search for. The subset of available options depends on the project type (.sqd vs. .assembly), assembly type (de novo vs. templated), and view in which the search is being done (Alignment vs. Strategy). The table below shows possible options in alphabetical order.
Search Target Description
Conflict Search for any conflicts between the read files and the consensus or reference sequence. This search type locates any base that differs from one or more bases in other sequences in the same column of the alignment. SeqMan Ultra will find and highlight single conflicting residue columns or consecutive groups of conflicting columns. These conflicts occur when the consensus cannot be called cleanly, so there are ambiguous calls in the consensus. Conflict is available for de novo assembly projects only.
Coverage Search for the edge of a region that is below the minimum threshold coverage. The coverage threshold can be customized in the Strategy Viewing and Coverage parameters dialog.
Go To consensus position Go to a specific numerical position on the consensus sequence.
Go to reference position Go to a specific numerical position on the reference sequence.
In all sequences Search for the query bases (text string) in all sequences: reads, reference (if any) and consensus.
In consensus Search for the query bases (text string) only in the consensus row.
In selected sequence Search for the query bases (text string) only in the currently selected sequence.
Reference features Searches for and selects the next or previous feature on the reference sequence. To see these features in the view, be sure to check the Reference > Features box(es) in the Tracks panel.
Sequence Performs a literal (perfect match) sequence search on the query typed into the text box at right. You can use IUB ambiguity codes in literal sequence searches, but these will match only the same ambiguity code in the sequence. For example, searching for “S”—the ambiguity code for G or C—will locate only S, and neither G nor C. This can be useful for locating specific heterozygotes. To search for gaps, enter a dash (-) into the text box.
Variant Locates bases that have been identified by SeqMan NGen’s SNP-calling detector as variants. Variant is available for reference-guided assembly projects only.
  1. If the search type requires it, enter the query bases (text string) in the text box before using the arrows. Otherwise, skip to the next step. In some cases, a box is provided to Allow ambiguity. Check the box if you want to include IUPAC ambiguity codes in your search.

If you type a query that is “too wide” for the search box, you can hover over the search box to view the entire query. Note that long query sequences may take considerable time to locate.

  1. Use the right/left arrows ( ) to jump to the next/previous find. After reaching either end of an alignment, SeqMan Ultra wraps around and continues searching from the other end.

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