Your English is a little confusing, but I can see three errors from a quick glance:

next until ($seed=~/[ACGTN-]/ && (!($seed =~ /\$seed/))) { 

# should be:
next unless ($seed=~/[ACGTN-]/ && (!($seed =~ /\$seed/)));
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And there's also a problem with the second half of that statement:

(!($seed =~ /\$seed/)));
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That's always going to evaluate as true - assuming $seed is never '$seed' - ie you're looking to match a literal by escaping the $. And if you meant to interpolate it, it will always be false because $seed always matches $seed ??

Please clarify. Also:

$i=$i+1; 
}until($i>682);#Line 29
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Delete this - your initial for loop covers the condition.

If you clarify what you are trying to do and supply some sample data input and expected output, that would help.

cLive ;-)

--
seek(JOB,$$LA,0);