miRNA: 3'- -GAGCGGCGgc----UCCGGU----UGCGUCAUag -5'
miRNA: 3'- gaGCGGCGGCU-----------CCGGUUG-CGUC-AUAG- -5'
miRNA: 3'- gaGCGGCGGCUC-CGGUUG---------CGUCAUag -5'
miRNA: 3'- -GAGCGGCGGCUCCGGUUGCGUCAUAG- -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 | |||||||
| 22846 | 5' | -57.8 | NC_005135.1 | + | 44205 | 0.66 | 0.872336 |
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Target: 5'- gCUCGCCGCaccaauGGGUCGaaucACGUAGUGa- -3' miRNA: 3'- -GAGCGGCGgc----UCCGGU----UGCGUCAUag -5' |
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| 22846 | 5' | -57.8 | NC_005135.1 | + | 25751 | 0.69 | 0.696092 |
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Target: 5'- -aCGUCGCCGAgcgaugauucuGGCUAACgGCGGaUAUCa -3' miRNA: 3'- gaGCGGCGGCU-----------CCGGUUG-CGUC-AUAG- -5' |
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| 22846 | 5' | -57.8 | NC_005135.1 | + | 148015 | 0.77 | 0.29376 |
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Target: 5'- -aCGCCGCCGAGuGCCAAUgaguuuugaGCAGUAg- -3' miRNA: 3'- gaGCGGCGGCUC-CGGUUG---------CGUCAUag -5' |
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| 22846 | 5' | -57.8 | NC_005135.1 | + | 151245 | 1.1 | 0.001922 |
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Target: 5'- gCUCGCCGCCGAGGCCAACGCAGUAUCa -3' miRNA: 3'- -GAGCGGCGGCUCCGGUUGCGUCAUAG- -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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