miRNA: 3'- gCCGGUUU-ACCag--CGUCuCUCGGacu -5'
miRNA: 3'- gCCGGUUu----ACCAGCGUCUCucGGAcu -5'
miRNA: 3'- gCCGGuuuaCCAGcGuCUCUCGGACU- -5'
miRNA: 3'- gCCGGUUUa------------CCAGCGuCUCUCG-GACU- -5'
miRNA: 3'- gCCGGUuuaCCAGCGucUCUCGGACU- -5'
Results 1 - 5 of 5 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 | |||||||
| 8884 | 3' | -55.3 | NC_002484.1 | + | 42172 | 0.66 | 0.707555 |
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Target: 5'- uGGCCGAAcUGGaaaaGCAG-GAGCCg-- -3' miRNA: 3'- gCCGGUUU-ACCag--CGUCuCUCGGacu -5' |
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| 8884 | 3' | -55.3 | NC_002484.1 | + | 12988 | 0.66 | 0.685798 |
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Target: 5'- aGGUCAGuuucuUGGUCGUAGAGuuCCUu- -3' miRNA: 3'- gCCGGUUu----ACCAGCGUCUCucGGAcu -5' |
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| 8884 | 3' | -55.3 | NC_002484.1 | + | 11285 | 0.67 | 0.630688 |
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Target: 5'- aGGCCca--GGUCuC-GAGGGCCUGAu -3' miRNA: 3'- gCCGGuuuaCCAGcGuCUCUCGGACU- -5' |
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| 8884 | 3' | -55.3 | NC_002484.1 | + | 4302 | 0.68 | 0.593149 |
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Target: 5'- uGGCCAGGauggcuucgcugcGGUUGCuGGGAGCgCUGGa -3' miRNA: 3'- gCCGGUUUa------------CCAGCGuCUCUCG-GACU- -5' |
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| 8884 | 3' | -55.3 | NC_002484.1 | + | 32887 | 0.73 | 0.30117 |
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Target: 5'- uGGCCAg--GGUCGC--GGAGCUUGAg -3' miRNA: 3'- gCCGGUuuaCCAGCGucUCUCGGACU- -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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