You still seem to have a bug occasionally. You report an offset of 75, but I make it to be 59?

#! perl -slw
use strict;

sub slidingMatch {
    my ($seq, $word) = @_;

    return "Complete match at $-[1]\n" if $seq =~ /($word)/;

    my @bestMatch;

    # Try matching start
    my $str = substr $seq, 0, 3;
    my $wordLen = length $word;

    while ($word =~ /$str/g) {
        my $tailLen = length ($word) - (my $start = $-[0]);
        my $subWord = substr ($word, $wordLen - $tailLen);

        next if $seq !~ m/^$subWord/;
        @bestMatch = ($start, $tailLen);
        last;
    }

    # Try matching end
    my $rword = reverse $word;
    my $rseq = reverse $seq;
    $str = substr $rseq, 0, 3;

    while ($rword =~ /$str/g) {
        my $tailLen = length ($rword) - (my $start = $-[0]);

        last if @bestMatch && $tailLen < $bestMatch[1];

        my $subWord = substr ($rword, $wordLen - $tailLen);

        next if $rseq !~ m/^$subWord/;
        @bestMatch = (length ($seq) - $start, $tailLen);
        last;
    }

    return "Partial match found at $bestMatch[0] for $bestMatch[1] cha
+racters\n" if @bestMatch;
    return "No match found for $word in $seq\n";
}

print slidingMatch 
#012345678 012345678 012345678 012345678 012345678 012345678 
'GAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCATTGA
+TGGAGGGAGACACA',
                                                           'CTGCCATTGA
+TGGAGGGAGACACAACGTACGT';
__END__
c:\test>junk
Partial match found at 75 for 24 characters
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