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#!/usr/bin/perl

...
$s .= 'b' x $pad;

print substr( $s, $pad, 10 ), "\n"; # qq was here

sub editcontig {
  my $rawseq = shift;
...
  $rawseq =~ s/[0-9]//g;
  return $rawseq;
}

if ( $goodseq =~ /([^actg]+)/ ) {
  die 'found unexpected character $1";
}