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A small proportion of sequences did not have a nucleotide for alignment, and a gap was inserted at that site.
A polymorphic site contains variant nucleotides in a small proportion of sequences, and a gap was inserted at the corresponding position in the remaining sequences.
A small proportion of sequences were obtained from the 3' end using the M13 forward primer.
However, in some cases this procedure only finds a motif in a small proportion of sequences, and if necessary the value of mt was increased so that a motif was found in at least half the sequences.
The most striking feature of the set of spruce consensus sequences is the small proportion of sequences under 600 nucleotides compared to the PGI5.0 pine sequence assembly (mainly derived from 5' reads) despite its much larger number of sequences.
In examining the taxonomic distribution of nr blastx hits for the unigenes, we identified only a small proportion of sequences with best blast hits or LCA assignments outside of the green plants.
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In addition, a small proportion of sequencing tags could be mapped to exon sequences, which are likely to be RNA degradation products.
Although there was ultimately no explicit test of library fragment composition in the present study, using the HindIII- MspI enzyme combination followed by size selection we observed a very small proportion of sequence reads that required adapter trimming (1.2%), suggesting that most fragments were larger than 100 bp and were thus suitable for GBS.
Compared to Z. tritici, the functional annotation of the predicted gene models in Z. pseudotritici, Z. ardabiliae, and Z. brevis showed a larger proportion of sequences with an attributed function and a smaller proportion of sequences with no functional evidences.
Telomere-like motifs of the Arabidopsis-type were detected in 1.1% (20 clones) while a smaller proportion of sequences belong to the satellite family pAv34 (0.9%, 16 clones), [EMBL: AJ242669] which is organized in tandem arrays at subtelomeric regions [ 33].
Since the second exome capture experiment was more specific, a smaller proportion of sequences were of mitochondrial origin, so even though the exomes were covered seven times greater in the second experiment, it only yielded an average of 18.2 × of mtDNA sequences where the first experiment yielded 7.5 ×.
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