223445 BG2A093.x1	51	7 	51	4	75	96	0 1	0	44
223446 BG2A073.x1	51	7 	51	4	43	95	0 1	0	44
223447 BG2A033.x1	51	7 	51	4	44	92	0 1	0	42
223448 BG2A693.x1	51	7 	51	4	45	93	1 1	0	43
223449 BG2A045.x1	51	7 	51	4	47	95	1 1	0	47
223501 BG2A034.x1	51	7 	51	4	47	95	0 1	0	46
223442 BG2A021.x1	51	7 	51	4	48	96	0 1	0	45 

##</code><code>##

223445 BG2A093.x1	51	7 	51	4 1	75	96	0 1	0	44
223446 BG2A073.x1	51	7 	51	4 2	75	95	0 1	0   43 
223447 BG2A033.x1	51	7 	51	4 1	44	92	0 1	0	42
223448 BG2A693.x1	51	7 	51	4 1	45	93	1 1	0	43
223449 BG2A045.x1	51	7 	51	4 1	47	95	1 1	0	47
223501 BG2A034.x1	51	7 	51	4 2	47	95	0 1	0	46
223442 BG2A021.x1	51	7 	51	4 1	48	96	0 1	0	45

##</code><code>##

#!/usr/local/bin/perl -w 
my $pre_ref_pos_b;
my $pre_ref_pos_e;
my $count

while (<>) {

   chomp;
   my ($r_no,$r_name,$r_len,$r_pos_b, $r_pos_e, $ref_seq_no, $ref_pos_b, $ref_pos_e, $rev, $no_match, $paired, $aln_score) = split;
   while (defined($pre_ref_pos_b) && defined($pre_ref_pos_e) eq $ref_pos_b && $ref_pos_e) {
   $count++;
   print $r_name,$count,$r_ref_pos_b,$ref_pos_e\n;
   }
   $pre_ref_pos_b = $ref_pos_b;
   $pre_ref_pos_e = $ref_pos_e;

  }
}