file1.txt contains
>sample1
ACTACTAGCTC
>sample2
CGATCGAACC
>sample3
CGTTGAACTGAA

file2.txt contains
>sample1
1 4 23 43 65 67 17 15 1 3 2
>sample2
23 43 65 12 34 54 76 2 9 12
>sample3
32 12 43 54 26 47 58 11 8 6 9 9