That's the only way I can think of ... but you can make it a bit easier on yourself.

my $goal = "uekasdh";
my $search = join "\\n*", split "",  $goal;
my $replace = "JJJJJ";

$line =~ s/$search/$replace/o;

[download]

--
TTTATCGGTCGTTATATAGATGTTTGCA

In reply to Re: Matching across newlines without stripping them out by TomDLux
in thread Matching across newlines without stripping them out by nysus

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