>perl script.pl
Match: GNN at 7
Match: GNN at 7
Match: GNN at 7
Match: GNN at 7
Match: GNN at 7
Match: GNN at 7
Match: GNN at 7
Match: GNN at 7
...
It seems my Perl's tr/// clears pos for all strings. Workaround:
use strict;
use warnings;
my %seq;
my $k = 0;
$seq{$k} = 'xxxxxxxGNNNxxxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxx
+xx';
# break up three character repeats, inserting spaces
while ($seq{$k} =~ s/([QGYN])\1\1/$1$1 $1$1/g) { }
while ($seq{$k} =~ m/([QGYN]{3,5})/g) {
my $saved_pos = pos($seq{$k});
printf("Match: %s at %d\n",
$1,
pos($seq{$k}) - length($1)-2*(substr($seq{$k}, 0, pos($seq{$k}))
+ =~ tr/ / /),
);
pos($seq{$k}) = $saved_pos;
}
Finally, a solution that works!