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Sequence analysis showed that bacteriophage 14/1 is a close relative of bacteriophage F8 (66 kb) [31], having an overall DNA identity of 87% (total average), spread throughout the genome.
Each new sequence was automatically validated as an extension of the initial fragment using the Cap contig assembly program included in the BioEdit software [ 68] with a minimum overlap between the two sequences of 50 bp, and a minimum DNA identity of 95%.
This sequence has no homology to complete coding sequences within the public databases, although the first 137 bp (100% DNA identity) of this CDS, 3' of uvrA, is included as unannotated sequence at the end of the GenBank entry for uvrA from library clone pJKD909, derived from N. gonorrhoeae (U34760).
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DNA identities of 100%, 82%, and 81% were observed between Maringá dog 1 sequences and N. helminthoeca, N. risticii, and N. sennetsu for the rpoB genes, respectively.
On the other hand, a search in non-redundant (nr) database for #5871 revealed 72.3% DNA identity to the cDNA of mouse that incorporates proteins involved in chromosome partitioning and cell decision [ 21].
This sequence is very similar (87% DNA identity) to the equivalent genes of T. scotoductus SA1, so it was expected that homologous recombination could take place between the plasmid and the chromosome.
Our version of mRFP had been codon optimized for expression in E. coli, giving the pair a DNA identity level of 75%.
Finally, there is a lower limit to the DNA identity level of the genes being recombined, with 56% being the lowest reported identity level that lead to successful chimera generation [ 29].
ISNfa1 of the IS 481 family was found in two copies with 99% DNA identity; ISNfa2 of the IS 5 family in eight copies with identities going from 72% to 99%; and ISNfap1, a partial element of the Tn 3 family, having 85% DNA identity with a copy found on N. farcinica larger plasmid.
In B. pseudomallei strain 1655 a prophage with extended similarity to GI 2 (95 99% DNA identity over ~95% of the length of GI 2; data not shown), is integrated at an alternative tRNA gene on chromosome 1 (tRNA-Arg as opposed to tRNA-Phe).
The Salmonella and Escherichia phages all shared 81 % DNA identity; the similarity of ViI with phiSboM-AG3 and LIMEstone1 was 66% and 599 %, respectively.
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