Choose method:

Normal similarity (fast)
Weak similarity (for promoter seq comparison, up to 10000 bp recommended for WEB)

No dynamic programming
Global alignment with tail gaps by dynamic programming
Global alignment without tail gaps by dynamic programming
Local alignment by dynamic programming

Block info only
Fine alignment
Alignment bounds, Block info and fine alignment

In direct chain only
In reverse chain only
In both chains

Use Java viewer

Note. To run applet viewer you need to include linux1.softberry.com in the list of your browser (see instruction).

Please note that using option based on dynamic programming with big sequences is very slow.

[Help] [Show advanced options] 
[Example]
[Example w/o visualization]