After you've read a line, the file pointer will naturally always be at the end of the line (= beginning of the next line). That is so because for every byte being read, the file pointer advances by one.

Try this to get the correct positions:

my @indx;
my $pos = 0;

while(<FH1>){
    my ($id, $seq) = split /\t/;
    push(@indx, "$id\t$pos");
    $pos = tell FH1;
}
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