\1 is a regular expression pattern that matches what the first capture captured. It makes no sense to use it outside of regular expressions as you did.

Perl script: 

s/^(ISA\~.*?\~.*?\~.*?\~.*?\~.*?\~.*?\~.*?\~)(..........)(....).(\~.*)
+$/$1${2}0$3$4/

[download]

Perl command: 

perl -i -pe's/^(ISA\~.*?\~.*?\~.*?\~.*?\~.*?\~.*?\~.*?\~)(..........)(
+....).(\~.*)$/$1${2}0$3$4/' PB385930.P0

[download]

ssh command: 

ssh ... 'perl -i -pe'\''s/^(ISA\~.*?\~.*?\~.*?\~.*?\~.*?\~.*?\~.*?\~)(
+..........)(....).(\~.*)$/$1${2}0$3$4/'\'' PB385930.P0'

[download]

Note the ' needed to be escaped when placed inside another ' literal.

In reply to Re: problems with backreference by ikegami
in thread problems with backreference by cdlaforc

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