Your output loop uses $index, and you set $index=0 after your calls to sorter. If you want the actual contents of your array without $index, you can do that this way:

foreach my $seq ( @allSeq ) {
    print "seq -->$seq\n";
}
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I suggest also that you use warnings and that you name the parameters to your subs:

sub sorter {
    my ( $line, $iter_sub, $inc_sub ) = @_;

    my $i = $iter_sub->($index);
    $allSeq[$i] .= $line;
    $index = $inc_sub->($index);
    print "in: $line\n";
}
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