Do those clustered miRNAs stem from the same primary  microRNA? If it does, promoter region is located at the upsteam of the primary microRNA(full length mRNA).  PlantCARE may small number of promoter information. Co-expression genes detection with primary microRNA and following with common motifs identification with MEME may work well.

Thanks your answer. Yingfeng.

These miRNAs belong to the same miRNA family but not the same primary miRNA. there is only about 300bp interval space between different miRNAs. these miRNAs have different expression pattern, I just want to predict the potential regulatory motif in each miRNA promoter sequence. The question is so short internal sequence between different miRNAs member. I am not sure how long sequence can present the proper promoter sequence. Could a promoter sequence of certain miRNA overlap another primary miRNAs?

If you think they are clustered they should have the same primary miRNA sequence. That's the idea behind clustered miRNAs. A different expression pattern is normal in clustered miRNAs so this doesn't tell you much. 

Usually, if they are 300 bp apart they are considered to be clustered but they don't have to be. The only correct way how to say this is to do an sequencing experiment directly in the nucleus before a pri-miRNA is processed.

Problematic part is that, as you asked, promoters can overlap. Another thing is they can be located several thousand nucleotides from a miRNA they regulate. Also there could be so called "silent" promoters which are usually not active but are regulated under certain conditions. 

You can take a look into these papers. It describes a lot about miRNA promoters/TSS identification and properties (especially the first one is quite nice). 

Article MicroRNA Transcription Start Site Prediction with Multi-obje...

Article microTSS: Accurate microRNA transcription start site identif...

Thanks Jan Oppelt very much! Your answer made me out of confusion. Thanks you for recommended papers.