The sub keyword will only define the subroutine once, and to be able to write on @flankseq it will hold a reference to the variable (because otherwise, @flankseq being lexical, it could be destroyed although the function always needs it). So while you create a new @flankseq in each loop, the function always uses the same one. This is demonstrated by: 

$\ = $/;
for (1..2)
{
  my $var = 1;
  print \$var, " created";
  sub function
  {
    print \$var;
  }
  function();
}

[download]
SCALAR(0x825d70) created
SCALAR(0x825d70)
SCALAR(0x96ec08) created
SCALAR(0x825d70)

[download]
The solution is to define seqstore outside of the loop (it's not actually required, it's just better practice) and pass the array as a paramater (as a reference, so that it is passed all at once). 
    sub seqstore {
        my ($flankseq, $mode, @rcd) = @_;
        if ($mode eq "Pos") {
            push (@$flankseq, $rcd[0]);
        } elsif ($mode eq "Freq") {
            push (@$flankseq, $rcd[0]) for (1..$rcd[1]);
        }
        return;
    }

[download]
Now you have to call the function like that: seqstore(\@flankseq, $mode, $seqEX,$F[2]);

More info on closures, and on references

In reply to Re: Array ending up empty when processing more than a single file by Eily
in thread Array ending up empty when processing more than a single file by TJCooper

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