To match overlapping regexes, use a look-ahead assertion: 
my $s = 'AGCTTCTTGCTTCTTGC';
#         ~~~~~~~~~
#                ~~~~~~~~~
while ($s =~ /(?=GCTTCTTGC)/g) {
    say pos $s;
}

[download]

There's something wrong with your input, though, there's no overlap and it matches just once even with the look-ahead. I modified it as shown in the sample.

Another possibility is to use index: 

my $s = 'AGCTTCTTGCTTCTTGC';
my $pos = -1;
while (-1 != ($pos = index $s, 'GCTTCTTGC', $pos + 1)) {
    say $pos;
}

[download]
($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

[download]

In reply to Re: Double check for positions by choroba
in thread Double check for positions by bisimen

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