Try:

my $hay = ...;
my $nee = 'AGGATACGCCAC';
substr(  $hay, $_+4, 1 ) eq 'T' and print substr( $hay, $_, length( $n
+ee ) ) for fuzzyMatch( \$hay,  \$nee, 3 );
[download]

Thank you, but does this incorporate both $nee1 and $nee2 in this case where there are 2 sequences to search for?

Thank you, but does this incorporate both $nee1 and $nee2 in this case where there are 2 sequences to search for?

You said:

$nee1 = AGGA
$nee2 = CGCCAC
#What I want is the following in regular expression: 

$hay =~ /($nee1)T[ATGC]($nee2)/
[download]

I used:

my $nee = 'AGGATACGCCAC';
## $nee1   ^^^^
## T?          ^^
## $nee2         ^^^^^^
[download]

What do you think the answer to your question is?

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