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The MMP13 promoter contains three PEA3 motifs (PEA3 sequences are potential Ets binding motifs) and Ets1 has already been shown to bind to one of these sequences by EMSA analysis [16], [48].
The ITS2 region was selected as a barcode candidate because ITS2 sequences are potential general phylogenetic markers and are widely used for phylogenetic reconstructions at both the genus and species levels [26] [30].
Repeat sequences are potential markers for lysogenic phage or transposon-mediated recombination events.
These sequences are potential exons (including 3′- and 5′- untranslated regions [UTRs]) of the Chrysemys genome that we want to annotate.
ITS2 sequences are potential general phylogenetic markers and have been widely used for phylogenetic reconstructions at both the genus and the species levels [ 40, 41].
In this study, we identified 13 domains and 28 motifs that occurred more frequently in the positive dataset than in the negative dataset, suggesting that these sequences are potential target sites for Hsp70s in rice.
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After identifying potential siRNAs and conserved miRNAs from the unique sRNA sequences, the remaining sRNA sequences were potential candidate miRNAs.
This choice was hypothesis driven; at this stage of the project, also non-exonic sequences were potential, although less probable, candidates for the B7 gene.
In our simulation, only those chromosomal positions that show heterozygous or homozygous variants with respect to the haploid reference sequence are potential variant alleles in a child of those parents.
We also identified unigene sequences that are potential targets for the candidate novel miRNA sequences in watermelon and pepo genomes (Table 2, Additional file 2).
These sites were selected to avoid disrupting conserved sequences, which are potential regulatory elements.
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