From your description, it sounds like you are parsing a 'fasta' format file line by line and, if it is evenly divisible by 3, join that to a string of sequences passing that test. I'm not sure, but if a single line of the sequence is divisible by 3, the entire sequence may not. The method below reads in an entire sequence at a time, and checks for mod 3 == 0, (evenly divisible by 3).

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new( -file   => "input1.txt" ,
                           -format => 'fasta');
my ($string, $valid, $invalid) = ('', 0, 0);
while ( my $seq = $in->next_seq() ) {
    if ($seq->length % 3 == 0) {
        $string .= $seq->seq;
        ++$valid;
    }
    else {
        ++$invalid;    
    }
}

open LOGFILE, ">", 'somefile' or die "Unable to open 'somefile' for wr
+iting. $!";
print LOGFILE "Found ", $valid + $invalid, " blocks, joined $valid of 
+them and left out $invalid.\n";
close LOGFILE or die $!;
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Chris