miRNA: 3'- cagGACCGGG-AGgUGGACaGGGAGCu -5'
miRNA: 3'- caGG---ACCGGGAGGUGGACa-----GGga-----GCU- -5'
miRNA: 3'- caGGACCGGG------AGGUGGAC-AGGgagCU- -5'
miRNA: 3'- -CAGGACCGGGAGGUGGACAGGGAGCU- -5'
Results 1 - 4 of 4 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 | |||||||
| 13029 | 5' | -61.2 | NC_003390.1 | + | 41317 | 0.66 | 0.391013 |
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Target: 5'- --aCUGGUCCaUUgGCCUGaCCCUCGu -3' miRNA: 3'- cagGACCGGG-AGgUGGACaGGGAGCu -5' |
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| 13029 | 5' | -61.2 | NC_003390.1 | + | 20904 | 0.67 | 0.302209 |
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Target: 5'- -aCCgauUGGCCCUCCACCUGgggaugCCacuagggCGGg -3' miRNA: 3'- caGG---ACCGGGAGGUGGACa-----GGga-----GCU- -5' |
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| 13029 | 5' | -61.2 | NC_003390.1 | + | 28126 | 0.69 | 0.223973 |
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Target: 5'- -aCCUGGCCCguaagcUCCACCUGcUCCa--GAa -3' miRNA: 3'- caGGACCGGG------AGGUGGAC-AGGgagCU- -5' |
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| 13029 | 5' | -61.2 | NC_003390.1 | + | 21905 | 1.08 | 0.00026 |
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Target: 5'- cGUCCUGGCCCUCCACCUGUCCCUCGAc -3' miRNA: 3'- -CAGGACCGGGAGGUGGACAGGGAGCU- -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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