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Sequence analysis revealed that the combined sequences covered an open reading frame of a putative ClPDI cDNA (1828 bp, EMBL no. HM641784).
Alignments and analyses for independent genes and combined sequences were conducted as described for amino acid sequences in the phylogenetic analysis.
In some serotypes it was possible to design primers using the combined sequences from both eastern and western strains within an individual serotype, which successfully amplified Seg-2 sequences from both major topotypes.
The conjunct fragments were subcloned into the psiCHECK-2M in which BamHI and XhoI sites were introduced so that the combined sequences were unidirectionally inserted downstream of the Renilla luciferase gene.
The combined sequences of all mt protein-coding genes yield alignment lengths of about 10 12 kbp, i.e. about 10-times the sequence amounts commonly used in the 1980s.
Stopcodons were left out of these combined sequences.
Two small clusters combined sequences from prokaryotes and plant genomes.
The combined sequences were then aligned by eye with M EGA LIGN™ (DNASTAR®).
All analyses for population genetics and demographic history were based on the combined sequences.
Combined sequences from both culture conditions were used for all subsequent analyses.
Of these, 4 contigs combined sequences from pool B, and one contig each combined sequences from pools A and C. We used BLASTX to annotate our Silene latifolia unigene sequences.
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