Table 1 The number of differences (above the diagonals) and percentage of differences (below the diagonals, in italics) between pairs of homologous sequences within and between isolates MA, MM, and CR in each of the four sequenced regions
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  • Pairs of sequences were aligned in ClustalW with default parameters. Substitutions and indels in the paired sequences were identified with a custom Perl script (see File S1), counting each indel as a single difference. The two differences between MA2 and CR2 at the hisB region, SNPs 400 bp apart, were confirmed by amplifying and sequencing a 1-kb segment containing them. The six differences between MA2 in the hisA region, five SNPs and one indel, are all within an interval of 400 bp. Differences between MA1 and MM1 and between MA2 and CR2 are in cells with heavy outlines. The distribution of differences within each region and the locations of individual genes are shown in Figure S1 and Figure S2.