cutseq allows you to cut out a region from your sequence by specifying the begin and end positions of the sequence to remove.
To remove bases 10 to 12 from a sequence gatta.seq and write to the new sequence file gatta2.seq:
% cutseq gatta.seq gatta2.seq -from=10 -to=12
To remove the first 20 bases from hatta.seq and write it to jsh.seq:
% cutseq -seq=hatta.seq -from=1 -to=20 -out=jsh.seq