If I understand your question correctly perl -i might also do the trick (see perlrun for details, or type perldoc perlrun on your machine if www.perldoc.com is down):

perl -i -p -e '
BEGIN {
print "what length?\n";
$sequenceLength = getc;
}
s/$/$sequenceLength/' seq.txt
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will print the same question you asked for and add it to all lines in the file seq.txt.

Note that your getccall will only fetch 1 character, so if I answer '33' to the first question, it will only add a '3'. You might want to replace the getc part with something like:

$sequenceLength = <STDIN>; chomp($sequenceLength);
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