miRNA: 3'- uuauGGAGC-GG-CGCUGUCC-GCg-----CCGU- -5'
miRNA: 3'- uuAUGG----AGCGGCgCU-GUCCG-----CGCCGu -5'
miRNA: 3'- -UUAUGGAGCGG-CGCU--------GUC-CGcgCCGu -5'
miRNA: 3'- uuaUGGaG-CGGCGCU--GUCCGcGCCGU- -5'
miRNA: 3'- -UUAUGGA--GCGGCGc--UGuCCGCGCCGU- -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 | |||||||
| 8916 | 3' | -60.4 | NC_002484.1 | + | 8115 | 0.66 | 0.443355 |
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Target: 5'- ---cCCUCGaCCgGCGACGGGcCGaagucaGGCAa -3' miRNA: 3'- uuauGGAGC-GG-CGCUGUCC-GCg-----CCGU- -5' |
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| 8916 | 3' | -60.4 | NC_002484.1 | + | 50751 | 0.66 | 0.424512 |
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Target: 5'- -cUGCCucggUCGCCGgGAcCAGGCccuggGCGGUg -3' miRNA: 3'- uuAUGG----AGCGGCgCU-GUCCG-----CGCCGu -5' |
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| 8916 | 3' | -60.4 | NC_002484.1 | + | 25339 | 0.66 | 0.406156 |
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Target: 5'- gGGUGCCUCGCCaGCGAaugggcuuCAGcGCuuGGCu -3' miRNA: 3'- -UUAUGGAGCGG-CGCU--------GUC-CGcgCCGu -5' |
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| 8916 | 3' | -60.4 | NC_002484.1 | + | 26528 | 0.67 | 0.379578 |
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Target: 5'- --aGCC-CaGCCGCGGgcCAGGC-CGGCAc -3' miRNA: 3'- uuaUGGaG-CGGCGCU--GUCCGcGCCGU- -5' |
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| 8916 | 3' | -60.4 | NC_002484.1 | + | 34622 | 0.71 | 0.216187 |
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Target: 5'- uAAUGCCUgaCGCUGCauuGC-GGCGCGGCGg -3' miRNA: 3'- -UUAUGGA--GCGGCGc--UGuCCGCGCCGU- -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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