#!/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          --------
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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