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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

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

GroupCountPalindrome lengthPaired t-test p-value
nativerandom
ALL14,8135.55.40.000004***
nested8305.25.30.50~
non-nested13,9835.55.40.000001***
Ale13145.55.50.93
Alesia215.85.70.75
Angela915.35.30.93
Athila10885.55.30.008**
Bianca4436.06.10.97~
Bryco295.85.90.95~
CRM4825.35.20.53
Galadriel495.45.10.40
Ikeros3485.55.30.10
Ivana10185.55.30.008**
Ogre15205.55.40.64
Phygy2855.35.30.94
Reina8525.45.40.67
Retand20785.45.30.37
Sire12255.45.20.001**
Tcn119475.55.40.001**
TAR4775.55.40.14
Tekay10295.45.40.61
Tork5175.65.80.05*~
  1. 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