miRNA: 3'- cCUG-AGCCG-----------GGAGaaUCUCCUAGGGc -5'
miRNA: 3'- -CCUGa---GCCGGGagaAUCUCCuAGGGC- -5'
miRNA: 3'- cCUGaGCCGG---GAGAAUCUCCU-AGGGc -5'
miRNA: 3'- -CCUGa-----GCCGGGagaauCUCCUAGGGc -5'
Results 21 - 24 of 24 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 | |||||||
| 5505 | 3' | -56.3 | NC_001798.1 | + | 131353 | 0.67 | 0.86489 |
|
Target: 5'- cGACgUCGGCgcccggcgcggCCUC--GGGGGAUCCCc -3' miRNA: 3'- cCUG-AGCCG-----------GGAGaaUCUCCUAGGGc -5' |
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| 5505 | 3' | -56.3 | NC_001798.1 | + | 139570 | 0.71 | 0.644933 |
|
Target: 5'- gGGACguggCGGCCU---UGGAGG-UCCCGa -3' miRNA: 3'- -CCUGa---GCCGGGagaAUCUCCuAGGGC- -5' |
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| 5505 | 3' | -56.3 | NC_001798.1 | + | 141603 | 0.69 | 0.799479 |
|
Target: 5'- cGGCgUGGCCgagUUCUUGGAGGAgUCCCc -3' miRNA: 3'- cCUGaGCCGG---GAGAAUCUCCU-AGGGc -5' |
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| 5505 | 3' | -56.3 | NC_001798.1 | + | 152052 | 0.66 | 0.922924 |
|
Target: 5'- gGGGCggcgcaCGGCCCac---GGGGGUCCCc -3' miRNA: 3'- -CCUGa-----GCCGGGagaauCUCCUAGGGc -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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