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All sequences were manually trimmed for vector.
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Electropherograms were manually trimmed of poor sequence data.
Residues 59 98 were manually trimmed from the alignment based on poor conservation.
CRISPR PCR products were sequenced as with MLSA amplicons and manually trimmed and checked for sequencing errors using Sequencher 4.9 (Gene Codes, Ann Arbor, MI, USA).
Resulting chromatograms were manually trimmed and checked for calling errors.
For the manually trimmed instances, where no trace data was available, the option –notrace was used as well.
The corresponding sequence alignments for multi-clade motifs were manually trimmed to 25 amino acids, including bordering residues, and submitted to Weblogo v2.8.2 [ 57] for visualization.
The tree for the heme pathway gene glutamate-1-semialdehyde 2,1-aminomutase (hemL/GSA-AT) was manually trimmed to remove a clade consisting of homologs for the related protein ornithine-delta-aminotransferase that was also recovered with the parameters used in this pipeline.
For each individual, the free-living recording was manually trimmed to the exact time point where the monitor had been detached.
The completed alignment was manually trimmed and edited in MEGA 4.0 [62].
The alignments were examined and manually trimmed to ensure alignment quality.
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