File1:


CLS_S3_Contig2721-139_168
CLS_S3_Contig2722-375_390
CLS_S3_Contig2725-323_362
CLS_S3_Contig2725-455_480
CLS_S3_Contig2728-117_144
CLS_S3_Contig2728-437_472
CLS_S3_Contig2729-119_130
CLS_S3_Contig2729-163_220
CLS_S3_Contig2730-181_202
CLS_S3_Contig2730-361_384
CLS_S3_Contig2731-824_843
CLS_S3_Contig2731-1150_1201
CLS_S3_Contig2735-571_636
CLS_S3_Contig2735-677_710
CLS_S3_Contig2735-775_810
.
.
.

##</code><code>##

File2

CLS_S3_Contig2721-142_169
CLS_S3_Contig6525-509_514
CLS_S3_Contig6525-493_502
CLS_S3_Contig6525-503_508
CLS_S3_Contig2977-365_376
CLS_S3_Contig2977-77_82
CLS_S3_Contig2977-83_90
CLS_S3_Contig4978-271_274
CLS_S3_Contig4978-385_388
CLS_S3_Contig2730-365_389
.
.
.

##</code><code>##

Output:
Genename(file1) start  end ** Genename(file2)     start	end

CLS_S3_Contig2721 139 168 ** CLS_S3_Contig2721 142   169
CLS_S3_Contig2730 361 384 ** CLS_S3_Contig2730 365   389    
.
.


##</code><code>##



while(<INPUT1>){
         chomp;
         my @id = split /\t/;
            if ($id[0] =~ /(.+?)\-(\d+?)_(\d+)/) {
            my @line_map = ("$1",  $2, $3);
            push @file_map, [@line_map];
     }
}

close(INPUT1);


while(<INPUT2>){
         chomp;
         my @map_id = split /\t/;
            if ($tg_id[0] =~ /(.+?)\-(\d+?)_(\d+)/) {
            my @tg_id = ("$1",  $2, $3);
            push @file_tg, [@tg_id];
    }
}  

     
   
          if (($from_tg == $from_map) && ($to_tg == $to_map)){

                print  join("\t",$two_geno_id, $from_map,$to_map,"<-Mapside**TGside->",$two_geno_id, $from_tg, $to_tg, $from_map_tg_range, $to_map_tg_range),"\n";
            $lines_1++;
            }
            elsif (($from_tg < $to_map) && ($from_tg > $from_map)){

                print  join("\t",$two_geno_id, $from_map,$to_map,"<-Mapside**TGside->",$two_geno_id, $from_tg, $to_tg, $from_map_tg_range, $to_map_tg_range),"\n";
             $lines_9++;

    }