Thank you! I have modified the script and it now works!

my @splicejoin = join('', @spliceout);
        
            open (MYFILE, '>>fasta');
            print MYFILE (">" . "$col_ID[$i]" , "@splicejoin" . "\n");
+    
            close (MYFILE);
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Many thanks for the quick responses and for pointing me in the direction about it not actually being whitespace; didn't realise I could do that. Thanks again.