#include <MsgBoxConstants.au3> ; to declare the Constants of MsgBox
Local $sRegex = "(?m)(>ref\|NC_\d+\|)( \[[^[\]]+\])( \[[^[\]]+\])( \[[^[\]]+\])( \[[^[\]]+\](?: \[[^[\]]+\])*)"
Local $sString = ">ref|NC_001133| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=I]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001134| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=II]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001135| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=III]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001136| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=IV]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001137| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=V]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001138| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VI]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001139| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VII]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001140| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VIII]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001141| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=IX]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001142| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=X]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001143| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XI]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001144| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XII]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001145| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XIII]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001146| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XIV]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001147| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XV]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001148| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XVI]" & @CRLF & _
"" & @CRLF & _
">ref|NC_001224| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [location=mitochondrion] [top=circular]"
Local $sSubst = ">\5\2\3\4[\1]"
Local $sResult = StringRegExpReplace($sString, $sRegex, $sSubst)
MsgBox($MB_SYSTEMMODAL, "Result", $sResult)
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for AutoIt, please visit: https://www.autoitscript.com/autoit3/docs/functions/StringRegExp.htm