I am implementing RNAhybrid with the following miRNA and target sequences.
>target ACGGGGGUUUATCGUAUC >mir GAUACGAUAACCCCGU
The output is as follow.
target 5' GUU 3' ACGGGG UAUCGUAUC UGCCCC AUAGCAUAG miRNA 3' A 5'
I think the result is obviously wrong because the following structure is more stable.
target 5' GU 3' ACGGGG UUAUCGUAUC UGCCCC AAUAGCAUAG miRNA 3' 5'
Where is the problem? Could export give some suggestions or ideas? THANKS!