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More permissive alignment algorithms may also reduce the proportion of fragments that cannot be aligned, but could increase spurious alignments in complex genomes such as maize.
The new sequence has an unusual N-terminal extension of ∼70 residues that cannot be aligned to reference G-proteins and which is characterised by proline-rich repeats.
Perhaps most interesting is the finding of increased polymorphism rates in regions that cannot be aligned against the A. lyrata genome, with a compound effect of distance to centromeres.
This alignment shows that the HSF1 from S. cerevisiae contains eleven amino acids in the DNA-binding domain that cannot be aligned against the DNA-binding domain of HSF4 from A. thaliana.
Reads that cannot be aligned are optionally discarded.
Unigenes that cannot be aligned to any database were further scanned by ESTScan [ 43].
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These peptides share so little sequence information that they cannot be aligned while maintaining their structure.
The GOT1Sd and GOT1Sr paralogs have not diverged substantially in the sequenced coding regions, but the third intron has diverged to the degree that much of it cannot be aligned between the paralogs (it also differs significantly in size-761 bp for GOT1Sd and 2723 bp for GOT1Sr in the SD population).
These comparisons show that most of the A. thaliana mitochondrial sequence cannot be aligned with genomes outside the Brassicales.
However, a recent report indicated that many human genome regions containing RNA structures cannot be aligned with the mouse genome [ 20].
The clear shortcoming of the core constraint is that at some level of divergence, core regions cannot be aligned correctly without insertions or deletions, hence methods without the core constraint are more suited to remote homolog recognition and alignment.
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that cannot be integrated
that cannot be repaid
that cannot be determined
that cannot be missed
that cannot be extracted
that cannot be rescued
that cannot be covered
that cannot be delayed
that cannot be estimated
that cannot be relieved
that cannot be tolerated
that cannot be found
that cannot be sustained
that cannot be supported
that cannot be seen
that cannot be avoided
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