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my %main;
my $mfile = prompt( "Main file?" );
...

close MAIN;
chomp @$_ for values %main;

my $afile = prompt( "Annotation file?" );
open ANNOT, '<', $afile or die "$afile: $!";

open OUTPUT, '>', 'output.txt' or die $!;

OUTER: while( <ANNOT> ) {
    chomp;
...
        }
    }
}

    Ms------Me
                        As------Ae

                        Ms------Me
    As------Ae

OUTER: while( <ANNOT> ) {
    chomp;
...
        print OUTPUT "$atag\t$mess";
    }
}

my( $first, $lastTag ) = ( 0, '' );
OUTER: while( <ANNOT> ) {
...
        print OUTPUT "$atag\t$mess";
    }
}

C:\test>664760-gen > 664760.main
C:\test>wc -l 664760.main
...

C:\test>wc -l output.txt
 112805 output.txt

#! perl -slw
use strict;
...
C:\test>wc -l output.txt
 112805 output.txt