file1 contains multiple alphabetic sequences:
AETYUIOOILAKSJ EAYEURIOPOSIDK RYXURIAJSKDMAO URITORIEJAHSJD YWQIAKSJDHFKCM HAJSUDIDSJSIAJ AJDHDPFDIXSIBJ JAQIAUXCNC
$ cat tst.awk NR==FNR { lgth = length($0) pos2char[substr($0,1,lgth-1)] = substr($0,lgth,1) next } { for (pos in pos2char) { if ( substr($0,pos,1) == pos2char[pos] ) { print next } } } $ awk -f tst.awk file2 file1 AETYUIOOILAKSJ RYXURIAJSKDMAO URITORIEJAHSJD JAQIAUXCNCVUFO