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All study activities were reviewed and approved by the Children's Hospital Boston Committee on Clinical Investigation under a model of implied consent that was based on the pre-existing norms for sharing in the community and in alignment with the published privacy policy and terms of use of the site that clearly inform the community about conditions for sharing data and privacy protections.
Following alignment with the published Drosophila genome, unique nucleotide polymorphisms present in rye mutants were pooled together as potential EMS-induced mutations (n = 26,224).
Using a recently published Chinook salmon complete sdY mRNA sequence (GB: KC756279), we were able to hypothesize a tiled alignment with the published OTY3 contig (GB: DQ393568.1).
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The 12S rRNA (rrnL) gene was assumed to start from the end of trnV, and its end was roughly identified by alignment with the three published dipluran sequences.
Also, the sequences derived from the genome data are in agreement with the multiple sequence alignment while the published old sequences create strange insertions and substitutions.
Genetic variation was assessed throughout the PCR amplicon used for qCHIP analysis by alignment of genomic DNA with the published gene sequence (CLC Workbench, CLC bio).
An alignment was also made with the published SSRs (Table 2).
The mutant design was based on hexokinase sequence alignments and structural data together with the published data on Hxk2 mutants [ 3, 13, 15, 21].
Alignment of the de novo assembly with the published carrot plastid genome [ 24] showed full-length coverage, with 99% identity relative to the published sequence including 49 nt of difference in cumulative sequence SNPs, and 433 nt of cumulative indels, with a maximum indel length of 20 nt.
The final alignment of these contigs was performed with the BioEdit (ClustalW) software together with the published genomic sequences of the DQB1∗06:02:01, DQB1∗06:37 (exon 2 only) and DQB1∗03 02 01 alleles (IMGT/HLA database, http://www.ebi.ac.uk/imgt/hla/).ac.uk/imgt/hla/
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