Addendum: $. aka $INPUT_LINE_NUMBER will also give the current line number when reading from a file handle.

Update

use strict;
use warnings;

while (my $sequence = <DATA>) {
    chomp $sequence;
    if ($sequence =~ /[^ATCG]/){
        warn "Sequence '$sequence' in line $. has invalid character af
+ter " . $-[0];
    }
    else {
        print "Valid sequence: '$sequence'\n";
    }
}

__DATA__
TAAGAACAATAAGAACAA
TAAGAACAATAAUAACAA
TAAGAACAATAAGAACAA
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Sequence 'TAAGAACAATAAUAACAA' in line 2 has invalid character after 12 at parse_dna.pl line 7, <DATA> line 2.