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