Hi, I recently use DECIPHER on nine 16S rRNA and eight functional genes to do microarray probe design. First I combine these target genes as DNAStringSet, and I use DECIPHER function named "OrientNucleotides" on my DNAStringSet to check the orientation of my target genes. Second, I use DECIPHER function named "AlignSeqs" on my DNAStringSet to align my target genes because I think their sequences lengths are different. After this, these target genes of my DNAStringSet are the same, and I use DECIPHER function named "BrowseSeqs" on my DNAStringSet and it showed a "webpage" which included these target genes and a "consensus". What is its meaning? Finally I use DECIPHER function named DesignArray on my DNAStringSet which has been aligned, and I get 151 microarray probes, but these probes connecting poly-T tail. What's the meaning of poly-T tail connecting these probes? Questions：

1. Is DECIPHER function AlignSeqs applicable on target genes of my DNAStringSet? What's the purpose and meaning of function AlignSeqs?
2. What's the meaning of DECIPHER function BrowseSeqs when it showed a webpage about my target genes and "consensus"?
3. When I use DECIPHER function named DesignArray on my DNAStringSet, should I use function AlignSeqs on my DNAStringSet first? The results of DesignArray on my DNAStringSet with or without AlignSeqs, which one is better?
4. Why are these poly-T tail connecting on every microarray probes? Does poly-T tail affect the specificity and sensitivity of my microarray probes?

Thank you.

Best regards,

Henry Luo