miRNA: 3'- -GGUGGUGGCGGaag--ACUAag--ACCGUc -5'
miRNA: 3'- -GGU-----GGUGGCGGAAGACUAAgAcCGuc -5'
miRNA: 3'- -GGUGGUGGCGGAAGacuAAGa-CCGUC- -5'
miRNA: 3'- -GGUGGUggCGGaaGa----CUAAGACCGUC- -5'
miRNA: 3'- -GGUGGUGGCGGAAGACUAAGACCGUC- -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 | |||||||
| 32253 | 3' | -54.1 | NC_007022.1 | + | 31613 | 0.66 | 0.969644 |
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Target: 5'- gCUAUCGCCGCCgguuaUGAUguuaUGGCGu -3' miRNA: 3'- -GGUGGUGGCGGaag--ACUAag--ACCGUc -5' |
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| 32253 | 3' | -54.1 | NC_007022.1 | + | 138425 | 0.66 | 0.966576 |
|
Target: 5'- cCCAgauucCCGCCGUCUUCUGGUUgUuGCu- -3' miRNA: 3'- -GGU-----GGUGGCGGAAGACUAAgAcCGuc -5' |
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| 32253 | 3' | -54.1 | NC_007022.1 | + | 37905 | 0.66 | 0.966576 |
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Target: 5'- uUCAUCAUCGCCUUU---UUCagGGCAGu -3' miRNA: 3'- -GGUGGUGGCGGAAGacuAAGa-CCGUC- -5' |
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| 32253 | 3' | -54.1 | NC_007022.1 | + | 164675 | 0.66 | 0.963296 |
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Target: 5'- aCUACCGaaGCUggCgaugcGAUUCUGGUAGa -3' miRNA: 3'- -GGUGGUggCGGaaGa----CUAAGACCGUC- -5' |
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| 32253 | 3' | -54.1 | NC_007022.1 | + | 3926 | 1.1 | 0.004278 |
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Target: 5'- uCCACCACCGCCUUCUGAUUCUGGCAGu -3' miRNA: 3'- -GGUGGUGGCGGAAGACUAAGACCGUC- -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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