My favorite trick for this sort of fuzzy matching is to combine bit wise xor and the transliteration operator (used in this context for counting). Consider:

use strict;
use warnings;

my $target = 'TGATTGAATCAAGGTGTTTT';
my $match = 'TGAT';
my $quality = 0.75;
my $matchLen = length $match;
my $matchNum = int ($matchLen * $quality);

for my $offset (0 .. length ($target) - $matchLen) {
    my $test = substr $target, $offset, $matchLen;
    my $matched = ($test ^ $match) =~ tr/\x00//;

    next if $matched < $matchNum;
    print "Found <$test> at offset $offset which matches in $matched p
+laces\n";
}

[download]

Prints:

Found <TGAT> at offset 0 which matches in 4 places
Found <TGAA> at offset 4 which matches in 3 places
Found <TGTT> at offset 14 which matches in 3 places

[download]
True laziness is hard work

In reply to Re: Pattern searching allowing for mis-matches... by GrandFather
in thread Pattern searching allowing for mis-matches... by MaroonBalloon

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