By default, the search tools are hidden. To display them, 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. 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 search bar drop-down menu to choose the item to search for.
Search Target Description
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.
Ambiguous Sequence Performs a sequence search on the query typed into the text box at right. Unlike the Sequence option, Ambiguous Sequence recognizes IUB ambiguity codes in the query. If you enter the query GATS, for example, you would find GATC, GATG and GATS.
Conflict 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.
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.
Coverage Locates areas with any amount of coverage, including depth=1.
Reference Features Locates features on the consensus sequence.
  1. If you choose either of the Sequence options, you will need to enter the query sequence (text string) in the text box before using the arrows. Otherwise, skip to the next step.

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 a sequence, SeqMan Ultra wraps around and continues searching from the other end.

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