miRNA: 3'- -UUCCGGGCGCGUCUCCGAAAUCGACU- -5'
miRNA: 3'- uuCCGGGCGCGUCuc----CGAAau----CGACu -5'
miRNA: 3'- -UUCCGG-GCGCGUCU----C-CGAAau-CGACU- -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 | |||||||
| 1118 | 5' | -57.7 | NC_000942.1 | + | 5879 | 1.06 | 0.000309 |
|
Target: 5'- aAAGGCCCGCGCAGAGGCUUUAGCUGAc -3' miRNA: 3'- -UUCCGGGCGCGUCUCCGAAAUCGACU- -5' |
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| 1118 | 5' | -57.7 | NC_000942.1 | + | 21127 | 0.68 | 0.242928 |
|
Target: 5'- -uGGCCCGCGCAGuuccccGCUUgcuccuGCUGu -3' miRNA: 3'- uuCCGGGCGCGUCuc----CGAAau----CGACu -5' |
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| 1118 | 5' | -57.7 | NC_000942.1 | + | 21484 | 0.66 | 0.369085 |
|
Target: 5'- uAGGGCCuCGCGUAGGauacGcGCUUggcGCUGGa -3' miRNA: 3'- -UUCCGG-GCGCGUCU----C-CGAAau-CGACU- -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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