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Forward and palindromic repeats larger than 20 bp were identified with the Comparative Repeat Analysis program [ 66].
Besides SNPs, 97 InDels (≥2 bp) were identified with 79 successfully designed for further PCR verification and population genotype analysis [ 31].
The bases of the resulting paired-end reads (101 bp) were identified with the Illumina BaseCaller; FASTQ files [ 34] were produced for downstream analysis of the sequence data.
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From 15 minicircles a minimum common region of 48 bp was identified, with little identity to that from other dinoflagellate minicircles.
Three of these private alleles in H. naniflora (Hn7116 [422 bp], Hn01135 [300 bp], and Hn00304 [179 bp]), one in H. minor (Hn00252 [224 bp]), and one in H. heterophylla (Hn00002 [297 bp]) were identified with a frequency greater than 10%, and these can be diagnostic in species identification when morphological characters are unavailable.
The three largest scaffolds (93,892 bp, 89,349 bp, and 46,146 bp) were identified as nucleomorph with a depth of coverage of ~7,000× and with a G + C content of ~20% (The mapping strategy for calculating coverage is described in the next section).
Open reading frames (ORF) over 200 bp were identified and extracted with the EMBOSS tool "getorf" in Galaxy.
A total of 3,573,824 SNPs and 404,090 indels (of length ≤50 bp) were identified through comparing KWP1 genome with human reference genome (hg19) [ 17].
8,460 L1 elements with length over 6000 bp were identified and used for alignment to generate LINE nucleotide base matrix.
Paired ends with a distance of >1000 bp were identified as outliers and also removed.
The SSRs with the minimal length of 14 bp were identified using WebSat [ 14].
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