miRNA: 3'- cccUCACUGGGGa--GUCCAuGGUAGau -5'
miRNA: 3'- -CCC-UCACugGGgAGUCCaUGGUAGau -5'
miRNA: 3'- -CCCuCa-----------CUGGGGAGUCC----AUGGUAGAu -5'
miRNA: 3'- cCCUCa--CUGGGGAGUCCAUgGUa---GAu -5'
miRNA: 3'- -CCCUCACUGGGGAGUCCAUGGUAGAU- -5'
Results 1 - 5 of 5 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 13045 | 5' | -55.5 | NC_003390.1 | + | 21855 | 0.66 | 0.668179 |
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Target: 5'- --uGGUGGCCCCagaCGGGU-CCAUCg- -3' miRNA: 3'- cccUCACUGGGGa--GUCCAuGGUAGau -5' |
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| 13045 | 5' | -55.5 | NC_003390.1 | + | 32110 | 0.68 | 0.546234 |
|
Target: 5'- uGGGcAGUGugCUgUUAGG-ACCAUCg- -3' miRNA: 3'- -CCC-UCACugGGgAGUCCaUGGUAGau -5' |
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| 13045 | 5' | -55.5 | NC_003390.1 | + | 17799 | 0.68 | 0.533234 |
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Target: 5'- aGGGuGguuuguaauuggGGCCCUUCAGGaccuUACCGUCUu -3' miRNA: 3'- -CCCuCa-----------CUGGGGAGUCC----AUGGUAGAu -5' |
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| 13045 | 5' | -55.5 | NC_003390.1 | + | 45371 | 0.69 | 0.45195 |
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Target: 5'- uGGAGcugGACCCCUCAGGUAgUGguggCUu -3' miRNA: 3'- cCCUCa--CUGGGGAGUCCAUgGUa---GAu -5' |
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| 13045 | 5' | -55.5 | NC_003390.1 | + | 38852 | 1.09 | 0.00076 |
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Target: 5'- cGGGAGUGACCCCUCAGGUACCAUCUAc -3' miRNA: 3'- -CCCUCACUGGGGAGUCCAUGGUAGAU- -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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