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Mapped loci in common between the two species were used to identify homologies between rainbow trout and Chinook salmon and confirm alignment with previous studies (Naish et al. 2013; Phillips et al. 2013).
A rapid sagittal localizer scan was acquired to confirm alignment.
To confirm that the Affymetrix probe sets were indeed specific for each gene we confirmed their alignment with the human and rat genomes using the BLAT tool [ 24] at UCSC [ 27].
It both confirms their alignment with Western Europe and, however paradoxically, their independence: until 1991, Slovenia had been subject to outsiders throughout its history.
The deletions were confirmed by alignment with the M. tuberculosis and M. bovis sequences.
The M. anisopliae MAT1-2 HMG-box domain [Pfam: PF00505] was also confirmed by alignment with other MAT1-2 sequences and also carries a conserved intron [ 22, 24].
For the other remaining cultivars in this group, the PCR products amplified with the Pina-D and Pinb-D primer sets were directly sequenced from both strands by SinoGenoMax Co., Ltd (http://www.sinogenomax.com/) and genotypes were confirmed by alignment with either known Puroindoline-D1 alleles or the NCBI blast website (http://blast.ncbi.nlm.nih.gov/).nih.gov/
The protein-coding genes (PCGs) were identified by the ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) and rRNA genes by BLAST searches, then confirmed by alignment with homologous genes from those of other booklouse and louse species (Additional file 3).
Most "double-hits" are confirmed by alignments with ARPAnno.
This region contains four gene models confirmed by alignments with Vitis vinifera cDNAs from public databases.
The gene structure was further confirmed by TBLASTN alignment with the Drosophila ANCE-3 protein.
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