miRNA: 3'- aaGU--GCCGGaGUAUUu-CAUCCGGCGa -5'
miRNA: 3'- -AAgUGCCGGAG----UAUuuCAu---CCGGCGa -5'
miRNA: 3'- aaGUGCCGGAGuAUUUCAU--------CCGGCga -5'
miRNA: 3'- -AAGUGCCGGAGUauuUCAUC-C-GGCGa -5'
miRNA: 3'- -AAGUGCCGGAGUAUUUCAUCCGGCGA- -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 | |||||||
| 30959 | 5' | -53.8 | NC_006556.1 | + | 16992 | 0.66 | 0.45801 |
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Target: 5'- -aCAauUGGCCaCAUAGccGUAGGCCGCc -3' miRNA: 3'- aaGU--GCCGGaGUAUUu-CAUCCGGCGa -5' |
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| 30959 | 5' | -53.8 | NC_006556.1 | + | 7256 | 0.67 | 0.384743 |
|
Target: 5'- cUUgGCGGCCUUggggGUGuuGUuaguGGCCGCg -3' miRNA: 3'- -AAgUGCCGGAG----UAUuuCAu---CCGGCGa -5' |
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| 30959 | 5' | -53.8 | NC_006556.1 | + | 11785 | 0.71 | 0.234729 |
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Target: 5'- -gCACGGCCUC-UGAGGUGucugcguuGGCCGg- -3' miRNA: 3'- aaGUGCCGGAGuAUUUCAU--------CCGGCga -5' |
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| 30959 | 5' | -53.8 | NC_006556.1 | + | 18507 | 0.72 | 0.180076 |
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Target: 5'- cUUUACGGCCUCA---AGUAGuGaCCGCa -3' miRNA: 3'- -AAGUGCCGGAGUauuUCAUC-C-GGCGa -5' |
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| 30959 | 5' | -53.8 | NC_006556.1 | + | 11632 | 1.06 | 0.000462 |
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Target: 5'- aUUCACGGCCUCAUAAAGUAGGCCGCUg -3' miRNA: 3'- -AAGUGCCGGAGUAUUUCAUCCGGCGA- -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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