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

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

Group	Count	Palindrome length		Paired t-test p-value
Group	Count	native	random	Paired t-test p-value
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~***

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

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