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.