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The anchored ITS alignment of the data set using SATé featured 296 taxa and 1,094 aligned positions, including 140 constant characters, 75 parsimony-uninformative changes, and 879 (80%) parsimony-informative positions (Fig. 4).
For the second approach, SATé returned a best-scored ITS alignment of 1,296 positions for 300 taxa (Alignment S2).
Bayesian analysis using the 5.8S re-included ITS alignment of the large data set without manual adjustment produced a phylogeny with moderate to strong support for many internodes (Fig. 5).
The whole ITS alignment of all 300 ITS sequences as generated by Clustal W was deemed to be of unsatisfactory quality as the 5.8S region of many sequences was appreciably misaligned.
The ITS alignment of Eddie et al [ 11] is available online [ 64].
The final ITS alignment of 48 sequences (clones) of A. × cornutum had 583 constant characters; 17 were parsimony-uninformative, and 27 were parsimony-informative.
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The Bayesian analysis of the ITS alignment involved the construction of a discrete phylogeographical scenario for the evolution of the Soldanella genus.
The restoration is unlikely to solve the riddles of Stonehenge's original purpose or the precise reasons behind its alignment to the rising of the sun at the summer solstice.
Each aligned sequence read is considered one hit at the 5′ end of its alignment to the reference assembly.
However, in both cases, the ITS sequences were aligned by relatively "heroic" methods, and a more conservative procedure might have kept many separate taxonomically overlapping ITS alignments instead of one large one.
At their nascency, the magnetic field showed a switchover of its alignment, disruption of flux tubes and a recovery on a time scale of about 30 days.
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