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In contrast, the repeat hits showed strong evidence of residue bias at each position.
We then analyzed nucleotide bias at each position so as to understand whether the cleavage sites of miRNAs had specific features for miRNA [ 31].
The usual preference for a U at the 5' - end of plant small RNA sequences [ 40] was not observed (see Additional file 2 for redundant small RNA nucleotide bias at each position).
Nucleotide bias at each position in novel miRNA candidates from in vitro-grown pear shoots at each position in (A) the 24 °C library, and (B) the 37 °C library.
For example, two novel miRNA, i.e. novel-miR16 and novel-miR20*, were found only at PS4 (Additional file 4).> Novel miRNA was analyzed for nucleotide bias at each position.
The nucleotide bias at each position of the 98 novel identified miRNA (Additional file 3: Table S2) shoved that the first nucleotide of the new miRNA genes tended to be (U) in general.
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Nucleotide bias analysis at each position showed that A and U mainly appeared at the beginnings and the ends of reads, while C and G occupied a very high percentage at the second position and the positions of 6-9th, which belonged to the "seed region" in other species [ 19, 20].
Additionally nucleotide bias analysis at each position showed the GC content had a high frequency in the 3rd, 7th, and 19th positions with percentages of 92.64%, 92.80%, and 93.27%, respectively, while it seldom appeared at the 4th, 5th, 8th, 11th, and 20th positions with percentages of 7.49%, 7.30%, 7.26%, 10.25%, and 7.34% in the adult bovine library, respectively.
Length distribution of P. tomentosa small RNAs obtained by high-throughput sequencing in HP libraries a: Nucleotide bias at A position of sRNA tags; b: Nucleotide bias at U position of sRNA tags; c: Nucleotide bias at C position of sRNA tags; d: Nucleotide bias at G position of sRNA tags.
The P-value measures the significance of the substitution bias at the position.
In this regard, and in reference to their "ping-pong" amplification biogenesis mechanism, secondary piRNAs have an adenine bias at nucleotide position ten (Brennecke et al. 2007).
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