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@gene_score = (
         [ "gene_name_0", "score_0" ],
...
            ...
         [ "gene_name_400", "score_400" ]
);

@gene_start_stop_chr = (
         [ "gene_name_0", "start_0", "stop_0", "chr_0" ],
...
            ...
          [ "gene_name_30000", "start_30000", "stop_30000", "chr_30000
+" ]
);

@results = (
         [ "gene_name_0", "score_0", "start_0", "stop_0", "chr_0" ],
...
            ...
         [ "gene_name_400", "score_400", "start_400", "stop_400", "chr
+_400" ],
);

for (my $a = 0; $a < scalar @gene_score; $a++) {
        for (my $b = 0; $b < scalar @gssc; $b++) {
...
        }
}