The quickest to implement would be using printf.
#!/usr/bin/perl
use strict;
use warnings;
foreach (<DATA>) {
chomp;
my @strings = split;
printf("%-1s %-13s\t%8s\n", @strings);
}
__DATA__
D. persimilis ggacaata
D. grimshawi tcg-----
D. simulans gg---agc
D. willistoni aaataaat
D. virilis tcg-----
D. sechellia --------
But you also have the option of using formats. Using a format would be an advantage if you need a repeated header and/or footer. If you don't then I would stick with printf.
UPDATE: clarified printf vs. format advantages
grep
One dead unjugged rabbit fish later...
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