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It has recently been reported using human myoblasts that aligned cell sheets reorganize themselves to match the alignment of the top sheet, generating a completely aligned 3D muscle tissue.
This implies that at least 80% of the reference organism subsequence had to match the alignment.
In such cases, the gene structure usually only needs to be changed to exactly match the alignment.
For the clinical CT and MRI scans, lesions were manually drawn onto the standard MNI template brain oriented to match the alignment of the scans.
We confirmed this conjecture based on random sampling of multiple alignment columns in the WPA so as to match the alignment lengths in the CDA, and as suspected, on average, the sampled WPA reduces the number of cases of asymmetric evolution as compared to WPA and yields a comparable fraction of asymmetric evolution as that for the CDA (Additional file 1: Table S3).
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In cases of single pair matches, the alignment of the contigs with the genome sequence helped strengthen the merges and improved the quality of the physical map.
We trimmed the alignment to match the aligned length of the Rhagoletis sequences and constructed phylogenetic trees (neighbour-joining, 1000 bootstrap intervals).
To further determine which topological differences were most influential, tests were repeated with the positions of topology-variable accessions alternately modified to match the full alignment topology.
CDS sequences were aligned to match the protein alignments codon-by-codon.
If a primary alignment matches the optimal alignment found by SSEARCH, it is a 'match'match
Using the secondary structure (including non-Watson Crick base pairs), it is thenon-Watson Crickghlight base pairs it the secondary structure that do or do not match is thenalignment, and the user can then edit the alignment to opossibletois matchighlight
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