miRNA: 3'- caaaaaAGAU----AUCGUCGUG---------UCAGGAG- -5'
miRNA: 3'- caaaaAAGaUAUC-GUCGUGUCAGGag -5'
miRNA: 3'- caaaaAAGa-UAUCGUCGUGUCAG-GAG- -5'
miRNA: 3'- -CAAAAAAGAUAUCGUCGUGUCAGGAG- -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 | |||||||
| 27308 | 3' | -44.9 | NC_005856.1 | + | 43097 | 0.66 | 0.999817 |
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Target: 5'- -----aUCUGguauUAGCAGCGCcauuggugaGGUUCUCa -3' miRNA: 3'- caaaaaAGAU----AUCGUCGUG---------UCAGGAG- -5' |
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| 27308 | 3' | -44.9 | NC_005856.1 | + | 2732 | 0.67 | 0.999489 |
|
Target: 5'- ----aUUCcAUGGaCGGCACAGUCUg- -3' miRNA: 3'- caaaaAAGaUAUC-GUCGUGUCAGGag -5' |
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| 27308 | 3' | -44.9 | NC_005856.1 | + | 64310 | 0.77 | 0.818672 |
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Target: 5'- ----aUUCagGUGGCGGCGCAGUCaCUCc -3' miRNA: 3'- caaaaAAGa-UAUCGUCGUGUCAG-GAG- -5' |
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| 27308 | 3' | -44.9 | NC_005856.1 | + | 79732 | 1.13 | 0.010968 |
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Target: 5'- aGUUUUUUCUAUAGCAGCACAGUCCUCa -3' miRNA: 3'- -CAAAAAAGAUAUCGUCGUGUCAGGAG- -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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