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The assembly and gap closure procedure resulted in 54 gap-free contigs spanning 23.4 Mb.
Remaining gaps in the scaffolds were closed by primer walking to yield a final assembly of 54 gap-free contigs.
BP and provides one of the longest gap-free series from Italy and the Mediterranean region.
The highly repetitive nature of the remaining gaps prevented us from reconstructing gap-free genomes.
We also produced a gap-free alignment by eliminating all positions harboring alignment gaps in the master alignment.
Final RBH orthologue sets (see Additional file 1) contained 3,723 conifer genes (average gap-free length = 510 bp) and 4,080 1 1 angiosperm genes (average gap-free length = 387 bp).
Two gap-free nucleotide alignments (817 bp and 1,221 bp) were generated.
The ultimate goal of genome curation is to produce a gap-free genome [ 42].
Thus, a fragment represents a local pairwise gap-free alignment of these two sequences.
Alignments are composed from gap-free segment pairs, so-called fragment alignments or just fragments.
Thus, the final alignment contained 333 gap-free amino acid positions.
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