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The remaining 553 mapped microsatellites were positioned on shotgun scaffolds by BlastN search.
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Conserved microsatellites spanning more than one element were positioned in the element with the longest overlap.
First, SNP markers were positioned on the consensus framework map developed for each cross using microsatellite markers.
Additionally, there were seven polymorphic microsatellites that could be positioned on the map and another two that could only be assigned to specific LG's by their female informative component because they were homozygous in the F1 male.
Twenty-six of the newly mapped microsatellite markers had previously been positioned on the genetic linkage map constructed by [ 16], and have been used to integrate the RH map and the genetic map.
Each of the three D1 genes is positioned within tandemly duplicated segments that include the intergenic regions and is delineated by GAT microsatellites.
Positions of nonhuman microsatellites were converted to the hg18 human assembly using the liftOver utility and chain files (Kent et al. 2003) available at the UCSC Genome Browser (Karolchik et al. 2003).
Chromosome locations for supercontigs and associated microsatellites were assigned based on the linkage map positions of the previously defined genetic loci.
The positions of the Taq I associated DNA from them the microsatellites were identified have added locating the microsatellites at the SNP linkage map constructed in this study (Additional files 2 and 4 in red color).
Microsatellites were determined from single genotype infections from which we had obtained reliable unambiguous gene sequence at all positions.
From the output files of SciRoKo (that generates microsatellite sequences, their position in the genome with start and end coordinates in chromosomes/scaffolds/supercontigs), distances between neighboring microsatellites were calculated in each species.
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