If it has U, than it is not DNA sequence, check the detail of the molecule.

For example, the attached pic is the same case, the left part is from silva and right part is from the silva reference to ENA. In silva this and most of the entries are enlisted as RNA molecule.

Hi Muhammad, Abhijeet Singh 's answer is correct.

Just to clarify, however, RNA always has Us instead of Ts. The four nucleotides in RNA are : A, C, G and U. While the four nucleotides of DNA are: A, C, G, T.

As you said, you downloaded 16S rRNA, not DNA, therefore you should expect Us.

Hope this helps.

Usually the double-stranded genomic ribosomal DNA (rDNA) or even the complete eucaryotic rDNA-transcription unit (18S rDNA + ITS1-spacer + 5.8S rDNA + ITS2-spacer + 28S rDNA) is sequenced for phylogenetic comparisons using universal (or special) rDNA primers. Therefore, the DNA sequences (AGCT) are given. The rDNA-molecule may contain introns (see also: Article Prokaryotic introns and inteins: A panoply of Form and function

However, the functional molecule in the organism is the rRNA (AGCU). If we assume that no RNA-editing takes place and no intron is present in the rDNA, it is a 1:1 translation of the rDNA-sequence (T-->U & removal of primer ends & removal of introns). If you are comparing rRNA molecules you may want to generate a secondary structure model of the molecule for alignments with other organisms. This is only carried out with the single stranded rRNA-molecules, as the rDNA is double-stranded and does not form a secondary structrure as present in the ribosome.

16s rRNA gene sequences are composed of RNA nucleotides, not DNA. RNA sequence nucleotides are (A, U, C, G), and DNA sequence nucleotides are (A, T, C, G). So while DNA sequences have "Ts" (thymine); RNA sequences have "Us" (Uracil).