miRanda is capable of doing this if you download it and use the command line version instead of using the website.

http://www.microrna.org/microrna/getDownloads.do

Miranda and RNAhybrid (Offline), are the best software's for target prediction of list of miRNAs.

I would say TargetScanS it is really a good tool with high citation and ease of use.

thanks to all. Miranda is working with custom list but I find targetScanS demanding miRNA ids so couldn't use it for custom designed predictions

You may try also mirWalk, which integrates different prediction tools and predicted/validated mirnas. 

Hello,

I would recommend mirWalk. It's a really good tool.

Good luck.

Venk

Can any one help me to understand miRdeep cut of score for selection of  novel miRNAs

Check out http://www.nature.com/natureevents/science/events/47533-microRNA_Analysis_Using_Next_Generation_Sequencing