I am trying to annotate a set of probes (Affymetrix) for a plant species. I used blastn to find the desired genome region for each probe. But the results confused me. Now I have several hits (with the same parameters such as identity and evalue) for each probe. What should I do now? What is your suggestion to solve this problem?
blastn -task blastn-short -evalue 0.0001 -db plant_genes -query plant_affy_probes.fasta -out outputfile.csv -perc_identity 100 -outfmt 7