Skip to main content

Table 2 Palindromes within sequences flanking the insertion site. We used the paldpl program to detect approximate palindromes of at least 3 bp with no more than 30% mismatches or indels. This analysis was done in native flanking sequences identified in plant genomes and their randomized (permutated) counterparts, to control for base content effects. We carried out a paired t-test for difference in calculated stem lengths of the native and randomized palindromes. Significant values after Benjamini-Hochberg correction for multiple family testing are marked with an asterisk and printed in bold (* for p < 0.1, ** for p < 0.01 and *** for p < 0.001). Three families with increased mean palindrome stem length after randomization are marked with a tilde

From: Correction to: Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Group Count Palindrome length Paired t-test p-value
native random
ALL 14,813 5.5 5.4 0.000004***
nested 830 5.2 5.3 0.50~
non-nested 13,983 5.5 5.4 0.000001***
Ale 1314 5.5 5.5 0.93
Alesia 21 5.8 5.7 0.75
Angela 91 5.3 5.3 0.93
Athila 1088 5.5 5.3 0.008**
Bianca 443 6.0 6.1 0.97~
Bryco 29 5.8 5.9 0.95~
CRM 482 5.3 5.2 0.53
Galadriel 49 5.4 5.1 0.40
Ikeros 348 5.5 5.3 0.10
Ivana 1018 5.5 5.3 0.008**
Ogre 1520 5.5 5.4 0.64
Phygy 285 5.3 5.3 0.94
Reina 852 5.4 5.4 0.67
Retand 2078 5.4 5.3 0.37
Sire 1225 5.4 5.2 0.001**
Tcn1 1947 5.5 5.4 0.001**
TAR 477 5.5 5.4 0.14
Tekay 1029 5.4 5.4 0.61
Tork 517 5.6 5.8 0.05*~