miRNA: 3'- -UACCCUGUGGUCCUGUGGUUUUUGUU- -5'
miRNA: 3'- -UACCcUG--------------UGGUCCUGUGGUUUUUgUU- -5'
miRNA: 3'- -UACCCUGUGguCCUG---UGgUUUUUgUU- -5'
Results 1 - 3 of 3 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 13917 | 3' | -51.1 | NC_003504.1 | + | 2536 | 1.04 | 0.000042 |
|
Target: 5'- uAUGGGACACCAGGACACCAAAAACAAu -3' miRNA: 3'- -UACCCUGUGGUCCUGUGGUUUUUGUU- -5' |
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| 13917 | 3' | -51.1 | NC_003504.1 | + | 2450 | 0.67 | 0.086913 |
|
Target: 5'- cGUGGcAUauuuguaaauaugaGCCAGGACACCAGGGGgGAg -3' miRNA: 3'- -UACCcUG--------------UGGUCCUGUGGUUUUUgUU- -5' |
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| 13917 | 3' | -51.1 | NC_003504.1 | + | 60 | 0.68 | 0.064498 |
|
Target: 5'- uAUGGGACACguGGACcaaGCgAGAGAgAGg -3' miRNA: 3'- -UACCCUGUGguCCUG---UGgUUUUUgUU- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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