miRNA: 3'- -ACCaUCGCGCCCUuc---UGGGGUCugUC- -5'
miRNA: 3'- -ACCAUCGCGcCCUUcu-GGGGUCUgUC- -5'
miRNA: 3'- acCAUCGCGCCCU------UCUGgGGUCuGUC- -5'
miRNA: 3'- -ACCAUCGCGCCCUUCUGGGGUCUGUC- -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 | |||||||
| 17966 | 5' | -58 | NC_004665.1 | + | 12701 | 0.67 | 0.366447 |
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Target: 5'- cUGGaAGCGUGGGGcuaucGCCUCGGugAGa -3' miRNA: 3'- -ACCaUCGCGCCCUuc---UGGGGUCugUC- -5' |
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| 17966 | 5' | -58 | NC_004665.1 | + | 5618 | 0.71 | 0.203287 |
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Target: 5'- aUGGUGGCGCuGGAGauuCCCCGGAaGGa -3' miRNA: 3'- -ACCAUCGCGcCCUUcu-GGGGUCUgUC- -5' |
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| 17966 | 5' | -58 | NC_004665.1 | + | 29779 | 0.74 | 0.142073 |
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Target: 5'- -aGUAGCGCGGGAagcguaGGACgCCAGcCAGc -3' miRNA: 3'- acCAUCGCGCCCU------UCUGgGGUCuGUC- -5' |
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| 17966 | 5' | -58 | NC_004665.1 | + | 1905 | 1.09 | 0.000306 |
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Target: 5'- cUGGUAGCGCGGGAAGACCCCAGACAGg -3' miRNA: 3'- -ACCAUCGCGCCCUUCUGGGGUCUGUC- -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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