miRNA: 3'- -CCUGCGACCGCGGUGGCCGCGGCGGC- -5'
miRNA: 3'- -CCUG-------CGA--CCGCgGUGGCCGCgGCGGc -5'
miRNA: 3'- -CCUGCGac-----CGCGGUGGCCGC-GGCGGC- -5'
miRNA: 3'- -CCUgCGacCGCGGugGCCgCGGCGGC- -5'
miRNA: 3'- -CCUGCGACCGCGg----UGGCCGcgGCGGc -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 | |||||||
| 15654 | 5' | -65.6 | NC_004064.1 | + | 5105 | 1.08 | 0.000005 |
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Target: 5'- uGGACGCUGGCGCCACCGGCGCCGCCGc -3' miRNA: 3'- -CCUGCGACCGCGGUGGCCGCGGCGGC- -5' |
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| 15654 | 5' | -65.6 | NC_004064.1 | + | 5154 | 0.69 | 0.020587 |
|
Target: 5'- gGGGCaggugcaGCUgcGGCGgCGCCGGUGgCGCCa -3' miRNA: 3'- -CCUG-------CGA--CCGCgGUGGCCGCgGCGGc -5' |
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| 15654 | 5' | -65.6 | NC_004064.1 | + | 5567 | 0.68 | 0.025831 |
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Target: 5'- gGGAUGCcaacaccGCGUCACUGGUGaUCGCCGu -3' miRNA: 3'- -CCUGCGac-----CGCGGUGGCCGC-GGCGGC- -5' |
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| 15654 | 5' | -65.6 | NC_004064.1 | + | 1425 | 0.68 | 0.025831 |
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Target: 5'- cGGGgGU--GCGCUugCGG-GCCGCCGa -3' miRNA: 3'- -CCUgCGacCGCGGugGCCgCGGCGGC- -5' |
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| 15654 | 5' | -65.6 | NC_004064.1 | + | 1828 | 0.67 | 0.030295 |
|
Target: 5'- aGGAUGCUGGCGCaggaaGUCGGCaaCGUCa -3' miRNA: 3'- -CCUGCGACCGCGg----UGGCCGcgGCGGc -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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