Im trying to blast specific short sequence only 5 nucleotides against 3UTR different mRNAs but so far no specific bioinformatic web based tool allows blasting for 3UTR. its worthless and time consuming to retrive each 3UTR of each gene and then make alignment so i would be thankful if you could guide me for blasting against only 3UTR of the genes. How one can blast specific motif short sequence against 3UTR of mRNA? is there any webtool or software that allows you to retrive 3UTR of many mRNAs and blast your sequence?

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