#!/usr/bin/perl

# http://perlmonks.org/?node_id=1172822

use strict;
use warnings;

$_ = do { local $/; <DATA> };

1 while s/^\S+  +(\S.*?\S)  .*\K\n.*?  \1(?=  )//m;

print;

__DATA__
1..1524    chromosomal replication initiator protein DnaA    NC_017524
+.1
1..1524    chromosomal replication initiator protein DnaA    NC_016768
+.1
1..1524    chromosomal replication initiator protein DnaA    NC_009565
+.1
1000808..1002415    oxidoreductase    NC_009565.1
1000808..1002415    oxidoreductase    NC_017528.1
1002441..1002704    hypothetical protein    NC_016934.1
1002812..1003792    peptidoglycan-binding protein ArfA    NC_017523.1
1002812..1003792    peptidoglycan-binding protein ArfA    NC_021194.1
1002812..1003792    peptidoglycan-binding protein ArfA    NC_018143.2
1002812..1003792    peptidoglycan-binding protein ArfA    NC_020089.1
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