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and here is another I put together to show me :

(line|entry) #, org.string, st. position of pal., length of pal., palindrome found

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
so for your sig : "TTTATCGGTCGTTATATAGATGTTTGCA" I get the following output:
1 TTTATCGGTCGTTATATAGATGTTTGCA 0 3 TTT 1 TTTATCGGTCGTTATATAGATGTTTGCA 2 3 TAT 1 TTTATCGGTCGTTATATAGATGTTTGCA 12 3 TAT 1 TTTATCGGTCGTTATATAGATGTTTGCA 13 3 ATA 1 TTTATCGGTCGTTATATAGATGTTTGCA 14 3 TAT 1 TTTATCGGTCGTTATATAGATGTTTGCA 15 3 ATA 1 TTTATCGGTCGTTATATAGATGTTTGCA 17 3 AGA 1 TTTATCGGTCGTTATATAGATGTTTGCA 20 3 TGT 1 TTTATCGGTCGTTATATAGATGTTTGCA 22 3 TTT 1 TTTATCGGTCGTTATATAGATGTTTGCA 12 5 TATAT 1 TTTATCGGTCGTTATATAGATGTTTGCA 13 5 ATATA 1 TTTATCGGTCGTTATATAGATGTTTGCA 16 5 TAGAT 1 TTTATCGGTCGTTATATAGATGTTTGCA 21 5 GTTTG
again works with any list passed as $ARGV[0] or with individual strings ala:
# echo "TTTATCGGTCGTTATATAGATGTTTGCA" | perl -ne ...
etc. and it does not match whitespace(s) as part of a reverse complementary match

In reply to Re^2: What one-liners do people actually use? by l3v3l
in thread What one-liners do people actually use? by TomDLux

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