>perl -wMstrict -le
"my $seq = 'xxxTATAATGyyyTatAtAtzzz';
 my $box = qr{ (?i) TATA [TA] [TA] [TAG] }xms;
 ;;
 my @TATAs;
 while ($seq =~ m{ ($box) }xmsg) {
   push @TATAs, [ $1, $-[1], ];
   }
 ;;
 print qq{matched '$_->[0]' at pos $_->[1]} for @TATAs;
"
matched 'TATAATG' at pos 3
matched 'TatAtAt' at pos 13

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Updates:

  1. Note: The character class definition  [T|A] in the OP is probably not what you want. The  | (pipe) character has no special meaning in a character class; it just represents a literal  | character, so the character class  [T|A] matches a single one of any of three characters: 'T', 'A' or '|'.
  2. Changed example code to use case-insensitive matching per OPed example. Note that in matching long strings, case-insensitive matching may impose a significant performance penalty; it may be better to convert all strings to a common case, then match without case sensitivity.

In reply to Re: positions of multiple matches by AnomalousMonk
in thread positions of multiple matches by Anonymous Monk

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