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Multiple allelic sequences of each candidate gene were aligned by the CLUSTAL W method (Thompson et al. 1994) using MEGA5.
Tunisian and Turkish T. annulata DNA samples were used as templates for PCR amplification (see Additional file 3) and multiple allelic sequences were identified for each locus.
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The IMGT/HLA database provides multiple alignment for the allelic sequences with allele B*070201 as a reference.
Multiple allele-specific probes, each labelled with a different D A pair, can be used for querying allelic sequences.
Many of these clusters contain multiple allelic variants, such that if probes were designed to only one representative sequence from each cluster they may not hybridize to all the alleles.
See Figure 2 for allelic sequences.
To account for multiple allelic states, indels were analyzed as class explanatory variables in PROC MIXED.
The reasons of this multiple allelic effects are only understood in part.
These were corrected, and the amended sequences were used for identification of allelic sequences.
To analyse allelic patterns of methylation at Avy, we performed bisulphite allelic sequencing [23] of the Avy IAP 5'LTR on tail DNA from yellow and pseudoagouti mice.
Allelic methylation patterns at nine candidate loci were assessed by bisulfite allelic sequencing.
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