miRNA: 3'- aCGACCCA------CACCUAGg---CAUGCUauga -5'
miRNA: 3'- -ACGACCCAC-ACCU---------------AGGcaUGCuaUGA- -5'
miRNA: 3'- acGACCCACACCUA-GGCa--UGCUAUga -5'
miRNA: 3'- -ACG---ACCCACACCua-GGC-AUGCUAUGa -5'
miRNA: 3'- -ACGACCCACACCUAGGCAUGCUAUGA- -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 | |||||||
| 29202 | 3' | -53 | NC_006150.1 | + | 9352 | 0.66 | 0.989681 |
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Target: 5'- aGCUGGGUaaugccGUGGGUCaugaGUAUGGa--- -3' miRNA: 3'- aCGACCCA------CACCUAGg---CAUGCUauga -5' |
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| 29202 | 3' | -53 | NC_006150.1 | + | 104073 | 0.66 | 0.985813 |
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Target: 5'- uUGCUGGGUGuUGGGaauggccgcggcuguUCCcaGCGcgGCUg -3' miRNA: 3'- -ACGACCCAC-ACCU---------------AGGcaUGCuaUGA- -5' |
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| 29202 | 3' | -53 | NC_006150.1 | + | 63401 | 0.69 | 0.951035 |
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Target: 5'- -cUUGGGUGUGGAUuCUGgagGCGGUAg- -3' miRNA: 3'- acGACCCACACCUA-GGCa--UGCUAUga -5' |
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| 29202 | 3' | -53 | NC_006150.1 | + | 151848 | 0.71 | 0.884946 |
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Target: 5'- cUGCucuUGGGUGUGGuugCUGaUGCGGUGCc -3' miRNA: 3'- -ACG---ACCCACACCua-GGC-AUGCUAUGa -5' |
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| 29202 | 3' | -53 | NC_006150.1 | + | 116053 | 1.09 | 0.008149 |
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Target: 5'- aUGCUGGGUGUGGAUCCGUACGAUACUg -3' miRNA: 3'- -ACGACCCACACCUAGGCAUGCUAUGA- -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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