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For most of the full-length IS element copies (n = 101, 83%) we could not identify direct repeats (Tables 1, 2).
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The shorter alleles contained 15 to 19 repeats, corresponding to amplicons in the range of 446 to 458 bp, whereas the larger alleles presented 30, 46, 48, 60 and 750 repeats (Table 2).
In this study, we identified a number of miRNAs derived from tandem repeats and low-complexity repeats (Table S1).
Interestingly, eight of the top-10 length-deviant domains occur as structural repeats (Table 3 and Table S1).
Additionally, we identified 370 simple sequence repeats (SSRs or microsatellites), of which 69% were trinucleotide repeats, followed by 27% dinucleotide and 4% tetranucleotide repeats (Table 4, Table S6).
The regions of difference between Schu S4 and NE061598 were divided into 2 types: small tandem repeats (Table 2) and rearrangements (Table 3).
Recombination primers for six representative repeats (Table 2) are listed in Table S1, and FASTA-formatted sequences of sequenced PCR products are available in Dataset S2.
The samples were also analyzed to identify their biological sex using the amelogenin gene and the X and Y chromosome specific alphoid repeats (Table 5).
Most of the candidates were expressed at very low levels while a significant fraction of those expressed at a higher level were associated with repeats (Table S9).
The amplified DNA was cloned using the TopoTA kit (Invitrogen), and individual clones were sequenced and analyzed for the presence of repeats (Table 1).
The vast majority of the microsatellite loci (96% for B1 and 99% for B2) were di- or tri-nucleotide repeats (Table 3).
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