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";
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.