miRNA: 3'- ccgCGGaGGGU---CCUGa--UGAGGUGGGc -5'
miRNA: 3'- cCGCGGAGGGUCCUgauga--GGuGGGC- -5'
miRNA: 3'- cCGCGGaGGGUCCUGaugaGgUGGGC- -5'
miRNA: 3'- cCG-CGgAGGGUCCUGA-------UGAGGUgGGc -5'
miRNA: 3'- -CCGCGGAGGGUCCUGAUGAGGUGGGC- -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 | |||||||
| 725 | 5' | -60.3 | AC_000019.1 | + | 4743 | 0.66 | 0.371084 |
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Target: 5'- --aGCCcCCCAgguGGACaugAUUCCACCCu -3' miRNA: 3'- ccgCGGaGGGU---CCUGa--UGAGGUGGGc -5' |
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| 725 | 5' | -60.3 | AC_000019.1 | + | 21228 | 0.66 | 0.337502 |
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Target: 5'- aGCGCUUCCCGGGGuucauggCC-CCCGa -3' miRNA: 3'- cCGCGGAGGGUCCUgauga--GGuGGGC- -5' |
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| 725 | 5' | -60.3 | AC_000019.1 | + | 18070 | 0.67 | 0.313802 |
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Target: 5'- aGCGCC-CCCGGGACg---UgACCUGg -3' miRNA: 3'- cCGCGGaGGGUCCUGaugaGgUGGGC- -5' |
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| 725 | 5' | -60.3 | AC_000019.1 | + | 8264 | 0.68 | 0.256183 |
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Target: 5'- cGCaGCgUCUCAGGACUcuggacaGCUCCAgCCu -3' miRNA: 3'- cCG-CGgAGGGUCCUGA-------UGAGGUgGGc -5' |
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| 725 | 5' | -60.3 | AC_000019.1 | + | 26552 | 1.09 | 0.000175 |
|
Target: 5'- aGGCGCCUCCCAGGACUACUCCACCCGc -3' miRNA: 3'- -CCGCGGAGGGUCCUGAUGAGGUGGGC- -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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