$ cat 1000161.pl 
#!/usr/bin/perl -w
use strict;

my $s1 = "AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTT";
print "$s1\n";

my $idx = -1;

my $start = 'ATG';

while (my $prefix = substr($s1, ++$idx, 3)) {
	last if length $prefix < 3;
	
	# check for start indicator
	next unless $prefix eq 'ATG';
	
	my $peptide = proteinseq(substr($s1, $idx));
	print "\nPEPTIDE <$peptide>\n";
	}

sub proteinseq {
	my ($dna) = @_;
	
	my $dna_seq = '';
	for (my $i=0; $i < length($dna)-2; $i +=3) {
		my $codon = substr($dna, $i, 3);
		print "$codon\t";
		$dna_seq .= $codon; # moved up a line
        # We're done if we found the ending codon
		return $dna_seq if ($codon =~ /TA[GA]|TGA/);
	}
    # We hit end of our dna fragment
    return $dna_seq . "***";
}

$ perl 1000161.pl
AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTT
ATG	TAG	
PEPTIDE <ATGTAG>
ATG	GGG	ATG	ACC	CCG	CGA	CTT	GGA	TTA	GAG	TCT	CTT	
PEPTIDE <ATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTT***>
ATG	ACC	CCG	CGA	CTT	GGA	TTA	GAG	TCT	CTT	
PEPTIDE <ATGACCCCGCGACTTGGATTAGAGTCTCTT***>