I have two files
file1:
file1
>string1Name1 >string2Name2 >string3Name3
file2
your assignment is not right.
$ awk 'BEGIN {FS=OFS="\t"} NR==FNR {a[$1]=$2; next} $1 in a {print a[$1],$2}' file1 file2 Name1 sequence1 Name2 sequence2