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The sequence databases used for alignment analysis were obtained from NCBI.
Local alignment analysis were also performed where segments of the sequence contigs were compared to the Optical map.
Homology and alignment analysis were conducted by using ClustalX version 1.8 (www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalX) and MegAlign (DNASTAR, Madison, WI, USA).
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Multiple sequence alignment analysis was performed using software CLUSTAL × 1.8.
Subsequently, multiple alignment analysis was performed with DNAMAN 6.0 software.
Similar nucmer alignment analysis was also carried out for the sequence generated for the same gene on the resequencing array platform and the reference sequence.
Multiple alignment analysis was performed with ClustalX.
Protein sequence alignment analysis was viewed through Jalview program [ 27].
A multiple alignment analysis was carried out on AP2 domain sequences from Hevea, Arabidopsis and Populus.
Multiple alignment analysis was performed on full-length AP2 domain sequences from Hevea, Arabidopsis and Populus.
Multiple sequence alignment analysis was performed using CLUSTAL W (1.83) (http://sbcr.bii.a-star.edu.sg/clustalw/).sg/clustalw/
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