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There was 100% alignment agreement for forward and reverse sequencing traces for each sample using the ClustalW sequence alignment program.
Phylogenetic trees were constructed using the ClustalW sequence alignment tool [23] from the EMBL-EBI server and displayed using the MEGA4 software [24].
Multiple sequence alignments were created using the ClustalW Sequence Alignment program at DDBJ [ 47].
Alignment of the amino acid sequences of Foxl2 from different species was performed using the ClustalW sequence alignment program.
Multiple sequence alignments were created using the ClustalW Sequence Alignment program of the Molecular Evolution Genetics Analysis software 5 (MEGA5; [ 27]).
After excluding some gaps, 13,749 nucleotides were aligned (Align_Set_1) for 19 Chondrichthyes species (including C. monstrosa), and 13,784 nucleotides were aligned (Align_Set_2) for 18 Selachii and Batoidea species using the ClustalW sequence alignment settings with few manual adjustments (Table 2).
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Amino acid sequence alignments were performed using the ClustalW multiple sequence alignment program [ 56] employing the sequence from the first NPA motif to the start of the C-terminus (when sequence data was available), and were manually optimized using the Bioedit software [ 57].
Amino acid sequence alignments were performed using the ClustalW multiple sequence alignment program [ 65] employing the full-length amino acid sequence, and were manually optimized using the Bioedit software [ 66].
Sequence alignment was performed using the ClustalW multiple sequence alignment platform from the European Bioinformatics Institute [ 55] and compared with NM_001553 (IGFBP7) sequence.
Protein sequence alignments were performed using the ClustalW multiple sequence alignment algorithm [ 87].
The analysis using the ClustalW multiple sequence alignment showed that fragments recovered from the PLA2 sequence produced by the cDNA E6d and described by Tsai et al. [ 37] displayed 94% sequential homology (Table 2), except for a unique fragment that was not found (VTDCNPK).
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