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Thus, sequences containing microsatellites were aligned against a local database of Symbiodinium sequences.
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Xicmp3024 was mapped to LG 6, Xicmp3025 to LG 3, Xicmp3045 to LG 2 and Xicmp3066 to LG 7. To confirm map locations of the new EST-SSR markers, the mapped EST microsatellite sequences were aligned against the rice genome.
The sequences for both mtDNA (COI) and for nuclear regions (microsatellite flanking regions) were aligned based on the criterion of maximum parsimony, using the program Malign, specifying a 3 1 change:gap ratio [ 96].
For the clones containing microsatellite motifs, forward and reverse sequences were aligned using the software Sequencher version 4.1.2 (Gene Codes Corporation, Ann Arbor, Michigan, USA), and primers were designed with Primer3 software (Rozen and Skaletsky, 2000).
The 5' noncoding sequence pairs were aligned using DiAlign2 for finding conserved microsatellites.
The sequences of each region were aligned to evaluate the presence of SNPs, indels or polymorphic microsatellites among the six cultivars.
B. anynana microsatellite DNA loci described in van't Hof et al. [ 6] were aligned and grouped using Sequencher 4.5.
Accordingly, microsatellite and RAD-seq marker sequences (where available) for each data set were aligned with Astyanax genome scaffolds using the same BLAST and filtering protocols used for our own data (above).
The sequences were aligned manually.
Sequences were aligned in Vector NTI.
Eyes were aligned to fixation point.
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