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For calibration, the input variables are changed manually to match the simulated depths with the observed depths.

If a noticeable misalignment was detected, the CT image volume was realigned manually to match the noAC-SPECT and CT-AC was performed followed by image recon (Table 1).

CRISPRs were assigned to the most proximal cas locus, in a few cases the repeat detected by CRISPRfinder was changed manually to match homologous CRISPR repeats.

Grey level of the background was adjusted manually to match a fixed standard, and an automated thresholding process was used to find the perimeter of the droplet.

N-/C-termini of ancestral sequences were modified manually to match those of the closest modern sequence (determined by branch length).

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An exception is the 25 °C extraction of the Sinemurian siltstone, where pyrite dissolution was manually disabled to match the experimental results (compare Fig. 7).

TaqMan™ MGB probes and primers for the canSNPs were designed using ABI Primer Express software and guidelines, with the exception that allele-specific probe lengths were manually adjusted to match melting temperatures [37].

As accession numbers for mature miRNAs were introduced only in release 6.0, files up to miRBase release 5.1 were manually curated to match (later) accession numbers.

Sequences for the putative Borrelia OmpA-like TM domains were then added to this alignment and manually adjusted to match the topology and β-strand positioning as predicted by PRED-TMBB.

The Infernal model used by RDP II is computed from a set of several hundred carefully chosen sequences, which were manually aligned to match the well-known secondary structure of the 16S rRNA.

Full-length protein sequences for ubiquitin, Parkin, Rab1A and Rab8A were retrieved from UniProt via the EMBL-EBI database retrieval service (Lopez et al, 2003), client with the Jalview Desktop (Waterhouse et al, 2009) and manually aligned to match observed phosphorylation site positions.

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