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On the other hand, we found that most of tandem duplications occurred by a one-gene mode, i.e. only one gene was duplicated in a one tandem duplication event.
On the other hand, we found that most of tandem duplication occurred by a one-gene mode, i.e. only one gene was duplicated in a one tandem duplication event as shown in Figure 6.
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But further analysis of their similarities demonstrated that most of the tandem clustered NAC pairs shared relative low similarities (mostly below 50%), which may exclude them from tandem duplicate candidates.
Most of the tandem repeats are pairs, although eight triples and two quadruples were also observed (supplementary table S5, Supplementary Material online).
As is shown in Table 5, the most abundant repeat type was dinucleotides (51.0%, 6,659), and the most common number of tandem repeats was 6 (24.4%, 3,179).
Satellite DNAs (satDNAs) are the most abundant class of tandem repeats.
For instance, the strongly expressed locus 3 tomato genes rbcS-3B and rbcS-3C [ 68] represented the most derived members of tandem arrays according to our dendrograms.
The most abundant type of tandem repeats were those with period sizes of 29, 35 and 70, which totalled 40% of all tandem repeats found and 56% of the tandem distributed sequence.
The most common type of tandem repeat had period sizes of 42, 14 and 12, which totaled 42% of all tandem repeats found in the mitochondrial genome (Additional file 3: Table S3).
In order to get the most accurate datasets of tandem duplicated genes in plants, we designed the following major steps to obtain the tandem duplicated genes from assembled pseudomolecules by procedures consisting of 26 in-house Perl and Python scripts.
The most studied groups of tandem repeats in genomes are microsatellites (patterns of ∼10 bp) and minisatellites (patterns of ∼100 bp) because of their use as genetic markers in forensics, parentage assessment, positional cloning and population and evolutionary genetics (1).
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