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In all their tests, the long copy outperformed the short copy by wide margins.
The long copy contains internal complementary repeats flanking capD and capF genes.
We then performed multiple alignments of these sequences using clustalw [ 36] in order to detect the longest copies.
An intact copy was defined as a sequence whose length was at least 99% of the length of the longest copy detected, and a partial IS was defined as a >500 bp fragment with >80% DNA identity to an intact copy.
(Data not shown for the long-copy, short-spacer subset).
We noticed that the longest copy that could represent the initial deleted progenitor is more than 1700 bp long.
The long-copy, short-spacer subset has a smaller proportion of perfect IRs relative to the full genome.
The longest copy (112) is 9021-bp long, including TIRs of 4246-bp and 4680-bp (5′ and 3′, respectively; see Additional file 1).
To investigate these questions, we constructed the long-copy, short-spacer set, consisting of all IRs with spacers less than 11 and copy lengths longer than 9.
The results are shown in Fig. 2 for the full set (data not shown for the long-copy, short-spacer set).
This holds true in both the S. cerevisiae genome and its RA randomizations, in both the full sets and the long-copy, short-spacer subsets.
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