perl -p -i -w -e

 cat .txt

 kllk
 nciuwbufcbew``````//.]];s[[..;
 klklkl

 x,dsncdk,;l,ex
 xw,eocxmcmck

 perl -p -i.bak -w -e 's/1/k/g' .txt

 cat .txt
 kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
 kllk
 nciuwbufcbew``````//.]];s[[..;
 klklkl

 x,dsncdk,;l,ex
 xw,eocxmcmck
 kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk

 ls
 .txt  .txt.bak  Needleman_Wunsch.pl  test.pl