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The ribosomal DNA sequences were manually aligned according to secondary structure; non-alignable regions were excluded prior to the phylogenetic analyses.
The deduced AA sequences of the sheep potential functional TRDV genes and in-frame pseudogenes were also manually aligned according to IMGT unique numbering for the V-REGION [ 27] (Fig. 2).
The deduced amino acid (AA) sequences of the sheep TRAV genes were manually aligned according to IMGT unique numbering for the V-REGION [ 27] to maximize percentage of identity (Additional file 6).
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Nucleotide sequences were aligned according to corresponding aminoacid alignment produced by MUSCLE (Edgar 2004), and frameshift mutations were corrected manually.
Obtained nucleotide sequences were manually aligned using MacClade 4 [ 29], according to the reading frame of the conceptually translated amino acid sequences.
The sequences were manually aligned and the alignments were concatenated.
Chromatograms were manually aligned and then peaks were partitioned into bins according to retention time values.
Comparing measurements from automated and manually aligned MRI and fibrin samples verified quantitation.
DNA sequences were manually aligned and submitted to GenBank (AY944426-AY944463).
COI sequences were manually aligned in Se-Al v2.0a11 [43].
In a few cases spots were manually aligned.
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