einverted

einverted

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einverted looks for inverted repeats (stem loops) in a nucleotide sequence.

Here is a sample session with einverted:

% einverted Input sequence: embl:hsts1 Output file [hsts1.inv]: Gap penalty [12]: Minimum score threshold [50]: Match score [3]: Mismatch score [-4]:

Mandatory qualifiers:

[-sequence] (sequence)

Sequence USA.

-gap (integer)

Gap penalty.

-threshold (integer)

Minimum score threshold.

-match (integer)

Match score.

-mismatch (integer)

Mismatch score.

[-outfile] (outfile)

Output filename.