Here's one way to do it, given an input string such as 'abcde'. The program tries matching the one-character substring, then the two-character substring, and so on until it fails to match or the entire input string has been matched.

#!/usr/local/bin/perl -w

use strict;

print "Name of file containing various random strings?\n";
chomp (my $file = <STDIN>);
open (MOTIF, "$file") || die "$!";

print "String to search with?\n";
chomp (my $blocks = <STDIN>);

my $motif;
{
    local $/;
    $motif = <MOTIF>;
}

my $i = 1;
my $re = substr($blocks, 0, $i);

while ($i <= length $blocks and $motif =~ /\Q$re/) {
    $re = substr($blocks, 0, ++$i);
}

chop $re if $i <= length $blocks;

print "$re\n";
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To handle an input string like '(a|b)(b|c)(c|d|e)', you could use a similar approach, perhaps storing the possible characters for each position in an array of arrays, and iterating over each sub-array to construct the regexes.