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chr1    3204563    3661775    -
chr1    3204563    3600000    -
chr1    3204500    3660000    -
chr1    3204000    3204001    -
chr1    3204563    3760000    -

Xkr4    chr1    3204562    3661779    -    3    457.217    1
Xkr4    chr1    3204562    3661779    -    3    457.217    1
Xkr4    chr1    3204562    3661779    -    3    457.217    1

my @file1 = ();
open(FILE, @ARGV[0]) || 
...
            }    
    }
}