There are many criteria, as they write in this post.

To try blastn - does it look hopeless or useless?

I saw also this page below. It doesn't tell me anything clearly about microRNA and ncRNA difference.

http://www.abcam.com/tag/non-coding%20rnas%20and%20micrornas

I found these 2 papers (see the right panel of the page for others):

Functional interactions among microRNAs and long noncoding RNAs.

http://www.ncbi.nlm.nih.gov/pubmed/24965208

Systematic transcriptome wide analysis of lncRNA-miRNA interactions.

http://www.ncbi.nlm.nih.gov/pubmed/23405074

and this DB:

lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA

http://www.ncbi.nlm.nih.gov/pubmed/24926662

– it may be useful. You can get rid of lnc-RNAs, or at least recognize them.

And if nothing helps, try Biomart - it contains a lot of human sequence information.

See this post C: GC content calculation

and Biomart URL Devon gave (at the bottom).

MY SUGGESTION: IS IT POSSIBLE TO PREDICT micro-RNAs?

There is a site https://sites.google.com/site/mirnatools/mirna-databases

I am not sure it is free, but we can try...

List of RNA structure prediction software

https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software#Inter_molecular_interactions:_MicroRNA:UTR

Question_biostars: How can I detect lncRNA?

How can I detect lncRNA? AND Is there any specific quality metrics for lncRNA-seq or miRNA-seq?

And also this site:

http://www.abcam.com/kits/microrna-database-and-target-predictor-resources