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Repeat analysis reveals 12 direct and 2 inverted repeats ≥ 30 bp with a sequence identity ≥ 90%.
These repeat analyses identified a substantial number highly conserved repeats ≥ 30 bp with a sequence identity of ≥ 90%.
Repeat analysis identified 12 direct repeats and 2 palindromes of ≥ 30 bp with a sequence identity of ≥ 90%% (Hamming distance of 3).
The table includes the number and location of the repeats ≥ 30 bp, with a sequence identity greater than or equal to 90% (i.e., Hamming distance of 3).
The maximal cluster length (maximum length of predicted enhancers) was set at 3000 bp with a sequence conservation score cut-off of 2. This set of parameters successfully predicted a series of conserved blocks, designated E1 E4 (see Figure 5), in human, chicken, mouse, and other species.
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Jako and co-workers library has 954 sequences registered, the longest sequence is 691 bp and the shortest is 50 bp with a mean sequence size of 355 bp [ 14].
Most of the sequences ranged from 500 to 900 bp, with an average sequence length of 652 bp with the longest EST at 877 bp.
Amplification with primers OXA-1F and OXA-1R yielded a 595-bp product with a sequence consistent with that of blaOXA-1 (8 ).
Size distribution analysis showed that, after trimming of vector and poor quality sequences, most ESTs (89%) were longer than 600 bp, with an average sequence length of 673 nucleotides (Additional File 2A).
Among them, Illumina sequencing technology, which generates large-scale reads (75 150 bp) with a high sequencing coverage at lower costs, has extensively been used for de novo transcriptome studies [ 9- 11].
Assembly resulted in three independent contigs (CP21_C1, 94,267 bp; CP21_C2, 56,052 bp and CP21_C3, 28,698 bp) with an average sequence coverage of more than 105 per consensus base.
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