miRNA: 3'- -UGGUAGUGGUAGAUG-------CaGUUC-AUC-CC- -5'
miRNA: 3'- ugGUAGUGGUAGAUGc-----AGUUCAU------CCC- -5'
miRNA: 3'- -UGGua---GUGGUAGAuGCAGUUCAUCCc -5'
miRNA: 3'- -UGGUAGUGGUAGAUGCAGUUCAUCCC- -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 | |||||||
| 17594 | 3' | -49.5 | NC_004466.2 | + | 4893 | 0.67 | 0.8888 |
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Target: 5'- uGCCAUCAUCAUCUACacuuuggGcCAGGaUAGaGGu -3' miRNA: 3'- -UGGUAGUGGUAGAUG-------CaGUUC-AUC-CC- -5' |
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| 17594 | 3' | -49.5 | NC_004466.2 | + | 26576 | 0.68 | 0.847819 |
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Target: 5'- -aCGUCACCAUCUACaaccucUCGGGUAuagucuGGGu -3' miRNA: 3'- ugGUAGUGGUAGAUGc-----AGUUCAU------CCC- -5' |
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| 17594 | 3' | -49.5 | NC_004466.2 | + | 37976 | 0.74 | 0.530528 |
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Target: 5'- aGCCuuggcCAUCGUCUcCGUCAGGUAGGa -3' miRNA: 3'- -UGGua---GUGGUAGAuGCAGUUCAUCCc -5' |
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| 17594 | 3' | -49.5 | NC_004466.2 | + | 5250 | 1.11 | 0.002624 |
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Target: 5'- uACCAUCACCAUCUACGUCAAGUAGGGu -3' miRNA: 3'- -UGGUAGUGGUAGAUGCAGUUCAUCCC- -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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