Here's one way, which needs a slightly convoluted way of figuring out the original positiion: 
  # break up three character repeats, inserting spaces
  while ($seq{$k} =~ s/([QGYN])\1\1/$1$1 $1$1/g) { }

  while ($seq{$k} =~ m/([QGYN]{3,6})/g) {
    print "Match: $1 at ", pos($seq{$k})
      -  length($1)-2*(substr($seq{$k}, 0, pos($seq{$k})) =~ tr/ / /),
+ "\n";
  }

[download]
If you already have spaces in your sequences, you'd have to use some other character.

Updated: Changed 5 to 6. I thought the original had a "5", but it was just the tiny fonts on my monitor.

In reply to Re: Perl regular expression for amino acid sequence by Thelonius
in thread Perl regular expression for amino acid sequence by seaver

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