dotletprogram. For a quick summary of
dotlet's less obvious commands, see the command summary page. There is also an examples page that shows you the kind of features that can be discovered with this program.
dotlet's menu bar:
dotletwill create one for you. When you're done, click the Ok button. Characters other than letters are ignored, so it is ok to cut-and-paste a sequence that has spaces or position numbers in it. Case is not important.
<' (up left), '
>' (down right), '
[' (up right), and '
]' (down left). When the display is zoomed, the cursor will not be updated at every keystroke, but the alignment window will.
dotletwill reverse complement one of the sequences and perform a second comparison. Each pixel is set to the best of these two scores. This enables to see structures like stem-loops, for example. The alignment window will also display the reverse complemented sequence.