miRNA: 3'- aCGCGUacuGUGCG-CUCCG-------GUUCUAG- -5'
miRNA: 3'- aCGcGUaCUGUG--CGCUCCGGUUC-UAG- -5'
miRNA: 3'- aCGCg---UACUGU--GCGCU--------------CCGGUUCUAG- -5'
miRNA: 3'- -ACGCGUAcugUGCGCuCCGGUUCUag -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 | |||||||
| 20899 | 5' | -55.1 | NC_004689.1 | + | 11906 | 0.66 | 0.730968 |
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Target: 5'- aGCGCGgauCAUGCgGAGGCaugauuuCGAGGUCg -3' miRNA: 3'- aCGCGUacuGUGCG-CUCCG-------GUUCUAG- -5' |
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| 20899 | 5' | -55.1 | NC_004689.1 | + | 36110 | 0.68 | 0.634748 |
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Target: 5'- cGCaCAcGACACcuGCGGGGCUAGGcAUCa -3' miRNA: 3'- aCGcGUaCUGUG--CGCUCCGGUUC-UAG- -5' |
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| 20899 | 5' | -55.1 | NC_004689.1 | + | 58912 | 0.68 | 0.63146 |
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Target: 5'- aGCGaccgAUGGCAgaUGCGAuucggggauggucgGGCCGGGAUCg -3' miRNA: 3'- aCGCg---UACUGU--GCGCU--------------CCGGUUCUAG- -5' |
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| 20899 | 5' | -55.1 | NC_004689.1 | + | 36164 | 0.69 | 0.558512 |
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Target: 5'- cUGCGCAUa--AUGCGcGGCCAGGAg- -3' miRNA: 3'- -ACGCGUAcugUGCGCuCCGGUUCUag -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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