StemLoop searches for
inverted repeats in your sequence after you choose a minimum stem length and
minimum and maximum loop sizes.
You must also specify a
minimum number of bonds per stem with G-T, A-T/U, and G-C scored as 1, 2, and
3 bonds, respectively. The stems found can be sorted by position, size (stem
length), or quality (number of bonds) and can be either filed or displayed on
the screen.
StemLoop tells you the number
of stems found for your settings of
minimum stem size,
maximum loop size,
minimum loop size, and
minimum bonds per stem.
If you feel there are too
many stems, you may reset the parameters without reviewing the stems found or
view only the best stems found. To view only the best stems, there must be
more than 25 stems found and you must sort them by quality or size.