2gqt+FAD+A+601   2i0z+FAD+A+501
1n1e+NDE+A+400   2qzl+IXS+A+449
1llf+F23+A+800   1y0g+8PP+A+320
1ewf+PC1+A+577   2a94+AP0+A+336
2ydx+TXP+E+1339   3g8i+RO7+A+1
1gvh+HEM+A+1398   1v9y+HEM+A+1140
2i0z+FAD+A+501   3m2r+F43+A+1
1h6d+NDP+A+500   3rt4+LP5+C+501
1w07+FAD+A+1660   2pgn+FAD+A+612
2qd1+PP9+A+701   3gsi+FAD+A+902

##</code><code>##

2gqt+FAD+A+601   2i0z+FAD+A+501    0.874585  0.785412
1n1e+NDE+A+400   2qzl+IXS+A+449    0.145278  0.589452
1llf+F23+A+800   1y0g+8PP+A+320    0.784512  0.341786
1ewf+PC1+A+577   2a94+AP0+A+336    0.362542  0.784785
2ydx+TXP+E+1339   3g8i+RO7+A+1     0.251452  0.365298
1gvh+HEM+A+1398   1v9y+HEM+A+1140  0.784521  0.625893
2i0z+FAD+A+501   3m2r+F43+A+1      0.369856  0.354842
1h6d+NDP+A+500   3rt4+LP5+C+501    0.925478  0.365895
1w07+FAD+A+1660   2pgn+FAD+A+612   0.584785  0.325863
2qd1+PP9+A+701   3gsi+FAD+A+902    0.874526  0.125453

##</code><code>##

2gqt+FAD+A+601   2i0z+FAD+A+501 0.785412
1n1e+NDE+A+400   2qzl+IXS+A+449 0.589452
1llf+F23+A+800   1y0g+8PP+A+320 0.341786
1ewf+PC1+A+577   2a94+AP0+A+336 0.784785  
2ydx+TXP+E+1339   3g8i+RO7+A+1  0.365298
1gvh+HEM+A+1398   1v9y+HEM+A+114 0 0.625893
2i0z+FAD+A+501   3m2r+F43+A+1 0.354842
1h6d+NDP+A+500   3rt4+LP5+C+501 0.365895
1w07+FAD+A+1660   2pgn+FAD+A+612 0.325863
2qd1+PP9+A+701   3gsi+FAD+A+902 0.125453

##</code><code>##

use warnings;
open AS, "data";
open AQ, "pattern.txt";
@arr=<AS>;
@arr1=<AQ>;
foreach $line(@arr)
{
    @split=split(' ',$line);
    foreach $line1(@arr1)
    {
     @split1=split(' ',$line1);
     if($split[0] eq $split1[0] && $split[1] eq $split1[1])
     { print $split1[0],"\t",$split1[1],"\t",$split1[3],"\n";}
   }

}
close AQ;
close AS;

##</code><code>##

while ($line = <AQ>) #file handler for pattern
{
   while ($line_data = <AS>)
    { #do the matching here.?
    }
}