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A lower-scored whole ITS alignment was also examined (Alignment S3).
The 5.8S re-included ITS alignment featured 1,544 positions for 296 taxa (Alignment S5).
For the second approach, SATé returned a best-scored ITS alignment of 1,296 positions for 300 taxa (Alignment S2).
Additional file 1: ITS alignment.
The ITS alignment of Eddie et al [ 11] is available online [ 64].
Eleven sequences fell outside these clades and were included in the ITS alignment that featured their closest BLAST match.
The 475 bp nuclear ITS alignment contained five distinct haplotypes (Table 3; Figure 3; GenBank sequence accession numbers HQ864695- HQ864699).
A tree from the nuclear ITS alignment is almost unresolved (data not shown), but ITS sequences helped pinpoint suspected hybridization.
The non-gap coded ITS alignment was 895 sites long, with 440 variable and 317 parsimony informative sites.
Moreover, we implemented our own programming for individual aligner according to its alignment features as well.
Its alignment suggests that it was an astronomical observatory.
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