I don't know why you put this URL, do you mean this one: https://www.ebi.ac.uk/Tools/msa/clustalw2/ ?

If you want to use ClustalW2 all you have to do is put all the sequences you want to align in the central windows in fasta format.

Example:

>seq1

ACGT

>seq2

ACCT

Select if your sequences are DNA or protein and submit.

If you are used to NCBI-Blast you have to know that the aligning algorithm is really different. Usually I use clustal to find out little differences between sequences which I know are similar. If they are not clustal is not the best aligner, so, please, pay attention to that

Thanks for your guidance but I have a problem with the answer. I paste the sequence there and of course I choose DNA but it didn't give me the answer. It said you need two sequences!

You can do a blast search against the ENA (European Nucleotide Archive) here: http://www.ebi.ac.uk/ena/search/#Search

ClustalW and Clustal Omega are programs for alignment of multiple sequences as Riccardo demonstrated in an earlier post..

THANKS, but i have still have problem with that.

Thanks, eventually, i overcome the problem.

Hi Atena EslamiSelect if your sequences are need two sequences then take one reference sequences and aligning with reference sequnce ,

Thanks