My two cents

use strict;
use warnings;
use File::Copy;

my $newfile = 'uuu.new';

open (FH , ">  $newfile");

foreach my $line (<DATA>){

    print $line . "\n";

    # remove digits and spaces
    $line =~ s/[\d\s]+//g;

    print " New line : $line \n";
    print FH $line . "\n";
}

close FH;

__DATA__
1 TCCAAGGATA AGTATGTAAA TACGGGGCGG GCTCTGGGAG GGGAGAGACT TTACAAAAAT
61 GAGGGCTTTT ATTTTCCATT TGGAACGTGG GACAACAGAC CACAACGCAA TTCCATTTTG
121 CAAGTCTTTC CAAGGGAGAA GCTGTTCAAC CACCCGTTTG GGGGATGAGT GAGCCGACAC
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