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

Here is a sample session with palindrome. Because there are a number of overlapping possibilities in this sequence, we choose a longer minimum repeat length:

% palindrome
Input sequence: embl:hsts1
Enter minimum length of palindrome [10]: 15
Enter maximum length of palindrome [100]:
Enter maximum gap between repeated regions [100]:
Number of mismatches allowed [0]:
Output file [hsts1.pal]:
Report overlapping matches [Y]:

Mandatory qualifiers:

[-insequence] (seqall)

Sequence database USA.

-minpallen (integer)

Enter minimum length of palindrome.

-maxpallen (integer)

Enter maximum length of palindrome.

-gaplimit (integer)

Enter maximum gap between repeated regions.

-nummismatches (integer)

Number of mismatches allowed.

[-outfile] (outfile)

Output filename.

-[no]overlap (boolean)

Report overlapping matches.