You can use bedtools intersect

Here are possible steps:

1. Create a bed file from .misa file

   cut -f1,6,7 your_file.misa > misa.bed

   • Cut the file taking just the columns 1, 6 and 7.
   • col1 is the chr name
   • col6 is the start coordinate of the SSR
   • col7 is the stop coordinate of the SSR

2. Create a gff file with only genic feature entry from your GFF file (of the genome)

   awk -F "\t" '$3=="gene"{print}' > genic.gff

   • cut the GFF file with -F (field separator as <tab>) and match column 3 to feature "gene" and take the whole line

3. Now, use bedtools intersect

   bedtools intersect -a misa.bed -b genic.gff