miRNA: 3'- auGAUGGUGa--GGGUGa-------AGACGAUUGc -5'
miRNA: 3'- aUGAUGGUGaGGGugAAGACGAUUGC- -5'
miRNA: 3'- -AUGa---UGGUGaGGGUgaAGACGAU-UGC- -5'
miRNA: 3'- augaUGGUGAGGGUGAAGaCGAuUGc -5'
miRNA: 3'- aUGAUGGUGAGGGUGaAGACG-----AUUGC- -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 | |||||||
| 6263 | 5' | -50.8 | NC_001844.1 | + | 97371 | 0.67 | 0.983524 |
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Target: 5'- -uCUACCAUgucCCCACggcguuugUUUGCUGGCu -3' miRNA: 3'- auGAUGGUGa--GGGUGa-------AGACGAUUGc -5' |
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| 6263 | 5' | -50.8 | NC_001844.1 | + | 68807 | 0.67 | 0.981453 |
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Target: 5'- gACUGCUGC-CCCuuUUUUGUUAGCGc -3' miRNA: 3'- aUGAUGGUGaGGGugAAGACGAUUGC- -5' |
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| 6263 | 5' | -50.8 | NC_001844.1 | + | 117338 | 0.68 | 0.96809 |
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Target: 5'- aUACcccgGCCGC-CCCGgaUCUGCUGuACGg -3' miRNA: 3'- -AUGa---UGGUGaGGGUgaAGACGAU-UGC- -5' |
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| 6263 | 5' | -50.8 | NC_001844.1 | + | 22871 | 0.71 | 0.891517 |
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Target: 5'- ---gGCCGCUCCCAUUUC-GCUuGCa -3' miRNA: 3'- augaUGGUGAGGGUGAAGaCGAuUGc -5' |
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| 6263 | 5' | -50.8 | NC_001844.1 | + | 33753 | 0.75 | 0.709824 |
|
Target: 5'- cGCUACCAUUCCCGCcUUUGUgucagUAACGu -3' miRNA: 3'- aUGAUGGUGAGGGUGaAGACG-----AUUGC- -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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