You should probably consider using printf. You may need to scan all of your files first to determine maximum column widths.

knoppix@Microknoppix:~/data$ perl -E '
> open my $inFH, q{<}, \ <<EOD or die $!;
> 01-16A1-325     01-16A1-325     01-16A1-325     01-16A1-325
> 01-16A1-325     01-16A1-325     01-16A1-325     01-16A1-325
> A     T     G     C
> 11     47     0     1
> 11     47     0     0
> 11     48     0     0
> EOD
> 
> while ( <$inFH> )
> {
>     printf qq{%15s%15s%15s%15s\n}, split;
> }'
    01-16A1-325    01-16A1-325    01-16A1-325    01-16A1-325
    01-16A1-325    01-16A1-325    01-16A1-325    01-16A1-325
              A              T              G              C
             11             47              0              1
             11             47              0              0
             11             48              0              0
knoppix@Microknoppix:~/data$
[download]

I hope this is helpful.