miRNA: 3'- gGG-GC-AGCCUu---AGCUGGUCC-GUCa---UG- -5'
miRNA: 3'- ggGGcAGCCUUAGCUGGUCCGU-------CAUG- -5'
miRNA: 3'- -GGGGCaGCCU----UAGCUGG-------UCCGUCaug -5'
miRNA: 3'- -GGGGCaGCCuuAGCUGGUCCG----UCAUg -5'
miRNA: 3'- -GGGGCAGCCUUAGCUGGUCCGUCAUG- -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 | 5' | -55.5 | NC_007022.1 | + | 132007 | 0.66 | 0.93683 |
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Target: 5'- aCCaCGuUCGGAuacuUCGACCAGGaUAGgaucGCg -3' miRNA: 3'- gGG-GC-AGCCUu---AGCUGGUCC-GUCa---UG- -5' |
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| 32253 | 5' | -55.5 | NC_007022.1 | + | 160578 | 0.67 | 0.931436 |
|
Target: 5'- -aCC-UUGGGAUUGACCAGGCGcucuuccGUAUg -3' miRNA: 3'- ggGGcAGCCUUAGCUGGUCCGU-------CAUG- -5' |
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| 32253 | 5' | -55.5 | NC_007022.1 | + | 155944 | 0.67 | 0.926289 |
|
Target: 5'- aCCCCGaCGGAucuuAUUGGCCgcgaaaaAGGCGGa-- -3' miRNA: 3'- -GGGGCaGCCU----UAGCUGG-------UCCGUCaug -5' |
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| 32253 | 5' | -55.5 | NC_007022.1 | + | 103030 | 0.71 | 0.732524 |
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Target: 5'- aUCCCG-CGGucUCGGCCAGGUgaaaGGUGg -3' miRNA: 3'- -GGGGCaGCCuuAGCUGGUCCG----UCAUg -5' |
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| 32253 | 5' | -55.5 | NC_007022.1 | + | 3963 | 1.12 | 0.002857 |
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Target: 5'- aCCCCGUCGGAAUCGACCAGGCAGUACu -3' miRNA: 3'- -GGGGCAGCCUUAGCUGGUCCGUCAUG- -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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