Ok so I partially solved this. The genomes i want to screen are saved as fna files and the genes i want to screen for are saved in txt files. Then I run this nested loop in Ubuntu that performs a Blastn of the genes against all genomes and creates an xls file for each gebe containing the results for the blastn of each genome. The word size is set to 28bp to mimic megablast for intraspecies screening.

mkdir results_folder
for txt_fil in *txt
do
echo $txt_fil
for fna_fil in *fna
do
echo $fna_fil
blastn -task blastn -subject ${fna_fil} -query $txt_fil -word_size 28 -outfmt "6 sseqid pident length gapopen qstart qend sstart send evalue bitscore" -out "$fna_fil".csv
echo Done with $fna_fil
done
cat *csv >> "$txt_fil".xls
rm *csv
mv *xls results_folder
echo Done with $txt_fil
done;