miRNA: 3'- cCUGGGCGGcGCGUaggUUACGUuUG- -5'
miRNA: 3'- -CCUGgGCGgCGCgUAGGUU--ACG----UUUG- -5'
miRNA: 3'- -CCUGGg-------CggCGCGUAGGuuACGUUUG- -5'
miRNA: 3'- ccUGGGCGGCGCGUA-GGUUa--CGUUUG- -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 | |||||||
| 7576 | 5' | -54.5 | NC_001962.1 | + | 124666 | 0.67 | 0.890038 |
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Target: 5'- aGGCCCGCC-CGCAaaaAGUGCAcACc -3' miRNA: 3'- cCUGGGCGGcGCGUaggUUACGUuUG- -5' |
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| 7576 | 5' | -54.5 | NC_001962.1 | + | 35781 | 0.67 | 0.883 |
|
Target: 5'- uGGAUgCGCgGCGgGUCCAAcuUGCcgcaAAACu -3' miRNA: 3'- -CCUGgGCGgCGCgUAGGUU--ACG----UUUG- -5' |
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| 7576 | 5' | -54.5 | NC_001962.1 | + | 856 | 0.73 | 0.546681 |
|
Target: 5'- cGGACCagugaacaGagGCGCGUCUggUGCAAACu -3' miRNA: 3'- -CCUGGg-------CggCGCGUAGGuuACGUUUG- -5' |
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| 7576 | 5' | -54.5 | NC_001962.1 | + | 27144 | 0.76 | 0.394324 |
|
Target: 5'- -uGCCCGUCGCGCGUaCCGGagcGCGAACg -3' miRNA: 3'- ccUGGGCGGCGCGUA-GGUUa--CGUUUG- -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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