use strict;
use warnings;

my $inputLines = <<LINES;
TAAGAACAATAAGAACAA
TAAGAACA.TAAGAACAA
TAAG-ACA.TAAGAA_AA
LINES

open my $inFile, '<', \$inputLines or die "Can't open file: $!\n";

while (my $line = <$inFile>) {
    chomp $line;
    next if $line !~ /([^ACGT])/;

    print "In line $.: $line\n";
    my $offset = 0;

    while ($line =~ /([^ACGT])/) {
        print "Found $1 at ", $-[1] + $offset, "\n";
        substr $line, 0, $-[1] + 1, '';
        $offset += $-[1] + 1;
    }
}

##</code><code>##

In line 2: TAAGAACA.TAAGAACAA
Found . at 8
In line 3: TAAG-ACA.TAAGAA_AA
Found - at 4
Found . at 8
Found _ at 15