The first sequence is the cds sequence and the second is the ffn seque
+nce.  The output is below this and you will notice that the last "int
+ron" at right edge (3 prime end) does not get printed out.  i.e. AAAA
+AAAA does not get printed out.  I realize now that this is something 
+I did not specify.
[download]

>1    ...(cds sequence)
ATGGGGGTCTCTCTCTCTCTCGTCTCTCATCTCT
[download]

>1    ...(ffn sequence)
AAAAAATGGGGGTCTCTCTCTCTCTCGGGGGTCTCTCATCTCTAAAAAAAA
[download]

Output: (I tinkered with the output the way I need it)
>1 
{ATGGGGGTCTCTCTCTCTCTC} is preceeded by
AAAAA
>1
{GTCTCTCATCTCT} is preceeded by
GGGG

I am not sure if this is an easy thing to fix...I don't like to take u
+p too much of your time...if this is too much to fix I understand and
+ I appreciate what you have done thus far.

Dr.J
[download]