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Even though this strategy requires re-arraying, there is no bias due to insert length compared to normalization by re-association [ 15] and therefore constitutes a useful alternative.
Both of the latter two cases had multiple best hits but resulted in different alignment choices probably due to insert size statistics, in turn due to the particular input read batch.
About 1,900 clones were not included in the contig assembly, primarily due to lack of high quality sequence data but also due to insert sizes less than 100 bp (< 1%) or empty clones/ E. coli sequences (1%).
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Local stress concentrations due to inserts are known to cause structural failure, and experimental pull-out tests show that the failure load can vary by 20% between batches of sandwich panels.
Based on the special model, a frequency equation to predict the frequency variation at both the targeted and off-target modes due to inserting a resonator into the enclosure is provided, and a method to constrain the worsened noise level at off-target modes is also discussed.
The distortion for each DCT coefficient is computed as follows: D = E 2 ⋅ Q 2 (18) E = 0. 5 - C - ⌊ C ⌋, if C ∈ c m 1. 5 - C, if C ∈ c R. The distortion due to inserting or removing D IR is computed as follows: D I R = 0. 5 - C 2 ⋅ Q 2, i f C ∈ c R ∪ c I n s (19).
The largest difference was between rrnB23S and rrnC23S, due to inserts of 22, 62, and 34-nt (Figure 2, Table 1) and 115 substitutions.
The 5-stranded versions may show further variations due to inserts at different points in the conserved core.
Due to ambiguous homologisation of certain nucleotide positions in the alignments we excluded parts of high variability which were mainly due to inserts in certain taxa from the alignments.
Several base positions have been excluded from the alignments of 18S rRNA, 28S rRNA and 16S rRNA (for details see Table 2) prior to reconstructing phylogeny due to inserts in certain taxa or due to high variability within the alignments (especially in the 28S- and 16S-fragment).
In this step, there are cases where, due to inserted bases in the sample that exactly repeat existing reference bases (short duplications), single alignments are rewritten as two overlapping read alignments, rather than simply divided in half, so that the single-alignment mapping results exactly match what would have been output in the two-alignment case.
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