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  1. or download this
    perl -nle 'tr/a-z/A-Z/;$l=length();for $m(3..$l){for $c(0..($l-3)){las
+t if $m+$c>$l;$f=substr($_,$c,$m);($r=reverse($f))=~s/s+//g;print "$.
+\t$_\t$c\t$m\t$f" if ($f eq $r);}}' example | more
  2. or download this
    1    TTTATCGGTCGTTATATAGATGTTTGCA    0    3    TTT
1    TTTATCGGTCGTTATATAGATGTTTGCA    2    3    TAT
...
1    TTTATCGGTCGTTATATAGATGTTTGCA    13    5    ATATA
1    TTTATCGGTCGTTATATAGATGTTTGCA    16    5    TAGAT
1    TTTATCGGTCGTTATATAGATGTTTGCA    21    5    GTTTG
  3. or download this
    # echo "TTTATCGGTCGTTATATAGATGTTTGCA" | perl -ne ...