We have aligned two groups of sequences with a short overlap using
the fragmetn assembly software. The total consensus length is about
500 bp. The second group of sequences is offset about 300 bp from
Now we would like to get a printout with identical nucleotides to
the consensus shown as a "-" and differences as the actual base.
We have tried to use pileup but it gives a completely different
and very poor alignment. Can you make a data file for the program
PRETTY that includes offset information for each sequence? Are
there alternate strategies to see these differences?