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You are speculating about sintheny region (alignment of genes) but you do not want to show the information in aligned form!
Based on the IGS1 rDNA region alignment of hybrid strains and the Z. rouxii CECT 11923 and CECT 10425, in this work, we developed a pair of Zygosaccharomyces hybrid-specific primers, HibZF/HibZR.
Open image in new window Fig. 6 Nucleotide sequences alignment: a ITS-1 region alignment of Contracaecum larvae (sequences were deposited to the GenBank database under the accession numbers (KX580602-KX580607). b ITS-2 region alignment of Contracaecum larvae (sequences were deposited to the GenBank database under accession numbers (KX580607- KX5806013).Samples are labeled according to host fish.
The concatenated trnS-trnG spacer and trnL-trnF region alignment was used to estimate a genealogical network with statistical parsimony [28].
Additional file 4L: Manually-curated foamy virus polymerase coding region alignment.
The 'putative control region' alignment had 293 sites, 41 of which were variable, and 13 were parsimony informative.
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Gene region alignments were manually reviewed and edited.
Repetitive region alignments from the PCR survey also used the above method (alignments in Additional file 1: Figures S4 S6).
N- and C-terminal encoding region alignments were concatenated for phylogenetic analyses of spidroin paralogs (Additional file 1: Figure S2).
Ancestral repeat (AR) alignments were built from the region alignments by extracting all columns that overlapped ARs>22% diverged from consensus as determined by RepeatMasker.
However, we believe that manual scrutiny of repetitive region alignments will remain popular and necessary until the ambiguity surrounding these alignments is resolved with superior technology.
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