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This is efficiently done because Socrates keeps track of the anchor locus consensus sequences.
Since we found evidence of recombination within the Hox1 anchor locus, we attempted to further extend these investigations.
The aim was to enrich linkage groups to achieve a joining (anchor) locus density <50 cM per joining locus.
Moreover, some fragments did not match the sizes expected for the anchor locus but were found to be significantly larger (fig. 2 A ).
The following primers were used to amplify the Hox1 anchor locus: forward, 5′-CATTCATTCATTCATTCGCCCTC-3′ and reverse, 5′-CGGTCTCGCCAGTTGTATCAAG-3′ (Tm = 58 °C).
To perform clustering a data structure containing the anchor locus (including a specific break point the last aligned position before the soft clipping starts), the re-aligned locus (including a break point) and a voting matrix for the re-aligned and anchor locus consensus sequence is used.
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For grasses, the database contains 1335 candidate anchor loci.
Overall, the total number of anchor loci amounts to 77 markers.
Such markers were considered as anchor loci, around which the map was developed.
Linkage groups were assembled into chromosomes based on the presence of anchor loci - SSR (Table 2) and DArT.
The segregations of SSR anchor loci were determined in an earlier study of the same mapping population [ 7].
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