perl -p -i -w -e

 1 cat 1.txt
 2 11111111111111111111111111111111111
 3 kllk
 4 nciuwbufcbew``````//.]];s[[..;
 5 klklkl
 6 
 7 x,dsncdk,;l,ex
 8 xw,eocxmcmck
 9 11111111111111111111111111111111111
10 
11 perl -p -i.bak -w -e 's/1/k/g' 1.txt
12 
13 cat 1.txt
14 kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
15 kllk
16 nciuwbufcbew``````//.]];s[[..;
17 klklkl
18 
19 x,dsncdk,;l,ex
20 xw,eocxmcmck
21 kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk
22 
23 ls
24 1.txt  1.txt.bak  Needleman_Wunsch.pl  test.pl