This may point you in a helpful direction:

use strict;
use warnings;

my $seq = 'GAATGTTTTAGCAATCTCTTTCTGTC' .
    'ATGAATCCATGGCAGTGACCATACTAAT' .
    'GGTGACTGCCATTGATGGAGGGAGACACA';
    
my $word = 'CTGGATAAGAATGTTTTAGCAATCTCTT';

print slidingMatch($seq, $word);

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) - $tailLen, $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";
}

[download]

Prints:

Partial match found at 8 for 20 characters

[download]

Update: fixed bug where worse end match replaced start match.

Update: fixed tail match position calculation bug (see BrowserUk's reply).

DWIM is Perl's answer to Gödel

In reply to Re: Searching for a word that may only exist in part by GrandFather
in thread Searching for a word that may only exist in part by seaver

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