miRNA: 3'- -GUCggAGUGGUCCuUAuGGUCCUUau -5'
miRNA: 3'- gucGGAG----UGGUCCUUAUGGUCcuuau -5'
miRNA: 3'- gUCG-------GAgUGGUCCUUaUGGUCCUUau -5'
miRNA: 3'- -GUCGGAGUGGUCCUUAUGGUCCUUAU- -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 | |||||||
| 28263 | 3' | -52 | NC_005902.1 | + | 73281 | 0.66 | 0.988622 |
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Target: 5'- cCAGggUCACCAGGcAUuCCAGGAGc- -3' miRNA: 3'- -GUCggAGUGGUCCuUAuGGUCCUUau -5' |
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| 28263 | 3' | -52 | NC_005902.1 | + | 167820 | 0.66 | 0.988622 |
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Target: 5'- --aCCUCuuuuACCAGGAAUACCAGu---- -3' miRNA: 3'- gucGGAG----UGGUCCUUAUGGUCcuuau -5' |
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| 28263 | 3' | -52 | NC_005902.1 | + | 72643 | 0.69 | 0.945026 |
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Target: 5'- gAGCaauuacaCUgACCAGGAGaACCAGGAGg- -3' miRNA: 3'- gUCG-------GAgUGGUCCUUaUGGUCCUUau -5' |
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| 28263 | 3' | -52 | NC_005902.1 | + | 72873 | 1.07 | 0.009809 |
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Target: 5'- cCAGCCUCACCAGGAAUACCAGGAAUAc -3' miRNA: 3'- -GUCGGAGUGGUCCUUAUGGUCCUUAU- -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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