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Clustered networks showed more motifs on average than uniform cultures.
Oligomers generated by randomly chosen 10 JASPAR CORE PPM collections were planted into randomly selected start sites, so that each sequence has eight motifs on average.
Although generally somewhat slower than Amadeus and Trawler, DREME discovers more than twice as many identifiable cofactor motifs on average compared with Amadeus, and almost 10 times as many as Trawler.
Conserved binding intervals have more matches to Sox motifs on average than non-conserved intervals or randomly chosen control intervals, indicating that an increased motif density may contribute to functional binding by group B Sox proteins and be an important facet in binding conservation.
The highly conserved intervals contain significantly more Sox motifs on average (mean = 4.53) than the binding intervals unique to D. melanogaster (mean = 1.29, p = 3.03e-193, Wilcoxon rank sum test with continuity correction), showing that the presence and number of Sox motifs is positively correlated with Dichaete binding conservation.
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However, #4 5 has the largest counts per motif (on average, around eight motif counts per motif mode; Figure 4; see additional file 1-Table S1).
More than 95%% of internal pTSS were associated with a sequence match to the AT-rich motif, on average at the same position as the input motif (Additional file 5: Table S4).
Of the 1733 analysed upstream sequences, more than 95%% possessed a 9 nt long AT-rich motif, on average at position −8 to −16 relative to the TSS (Fig. 2a, Additional file 5: Table S4).
Moreover, compared to k-mers + motifs (0.793 on average), the average accuracy of IT (0.786) is almost as equal whereas k-mers + IT (0.803) perform slightly better.
The latter two are known to be implicated in the mutability of a sequence with CpG motifs occurring on average once every 64 base pairs and mutate at a rate that is ten times higher than that of other single base sites [ 27, 28].
Plants expressing a truncated allele of POT1A lacking the N-terminal OB motifs have, on average, 1 1.5 kb shorter telomeres [77], and the complete absence of POT1A results in an ever shorter telomeres (EST) phenotype, identical to the inactivation of telomerase [41].
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