STEMLOOP
StemLoop finds stems (inverted repeats) within a sequence.
You specify the minimum stem length (number of nucleotides in a paired stretch), minimum and maximum loop sizes, and the minimum number of bonds per stem (length of nucleotide sequence between the paired regions).
217 AGGCTGCAGTG AGCCGTGAT 11, 25
    |||||| ||||          C
257 TCCGGCCTCAC GTCACCGCG 
start
end
quality
size
stem
Vertical bars ('|') indicating the base pairs. The associated loop is shown to the right of the stem. If either the stem or loop is too long to be displayed in its entirety on the line, then only that part that fits on the line is shown. The first and last coordinates of the stem are displayed on the left, and the length of the stem (size), the number of bonds in the stem (quality), and the loop size are shown on the right.