diffseq problems

[Obi Griffith]

I have been having two problems with your diffseq program.  I am using 
command line diffseq from the EMBOSS-2.5.0 package.

1) using the -columns option doesn't have any effect on the output.  ie. 
  I can't get the nicely formatted tabular data promised:

# Report of diffseq of: AF129756 and AP000504

# AF129756 overlap starts at 6036
# AP000504 overlap starts at 1

# (AF129756) start end length sequence  (AP000504) start end length sequence

6882    6882    1       't'     847     847     1       'a'
7830    7830    1       'a'     1795    1795    1       'g'
8307    8307    0       ''      2273    2273    1       't'
8500    8500    1       'a'     2466    2466    1       'g'
8688    8688    0       ''      2655    2658    4       'tgtg'

2) I get the following errors:

Find differences (SNPs) between nearly identical sequences
Input sequence:AF129756
Second sequence:AP000504
Word size [10]: 2
Output report [1.diffseq]:
Warning: bad /replace value 'T'
Warning: bad /replace value 'C'
Warning: bad /replace value 'C'
Warning: bad /replace value 'T'
Warning: bad /replace value 'C'
Warning: bad /replace value 'GCCTT'

Any idea what's going on here?

Obi.