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The overall consensus binding motif was obtained by multiple alignments of the significant binding sequences with ClustalW, and it was visualized with SeqLogo program.
Conserved elements, as defined by multiple alignments of 44 vertebrate species, and repetitive element data sets were also downloaded from the UCSC Genome Browser.
We therefore probed relationships among 3' end sequences of mature C. elegans miRNAs by multiple alignments of the 3' sequence of each miRNA against 3' sequences of all the remaining miRNAs.
In addition, 18 SNPs differed between the A and C genomes, as shown by multiple alignments of 16 FAE1 sequences from the three Brassica species (Table 4).
Linker regions were determined by multiple alignments of fusion sequences with corresponding free-standing domains present in the closest relatives to organisms that lack the gene fusions.
Analysis of the rice MAPKKKs along with the Arabidopsis for Raf specific signature GTXX (W/Y) MAPE was carried out by multiple alignments of kinase domains.
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Degenerate PCR primers were designed by multiple alignment of the protein sequences of known structural genes encoding the catalytic subunits of NiFe-hydrogenases obtained from Swiss-Prot Protein Sequence Database through CLUSTAL-W software and compared for conserved sequence motifs.
A degenerate primer pair specific to catA sequences was designed by multiple alignment of known sequences coding a key intermediate of the β-ketoadiapate pathway degrading catechol, namely catechol 1,2-dioxygenase.
Two SNPs (Single Nucleotide Polymorphisms) were identified within exon 8 by multiple alignment of DNA sequences obtained from 24 bulls: a transition G/A (SNP 1181) and a transversion A/T (SNP 1299).
60% of the A. nidulans genome was covered by multiple alignment of 2 more genomes.
40% of the A. nidulans genome was covered by multiple alignment of all 7 genomes.
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