miRNA: 3'- -UUAGCuGGUAAAG---AAGGUaGUGGGCC- -5'
miRNA: 3'- -UUAGCUGGUAa------AGAAGGUAGU----------GGGCc -5'
miRNA: 3'- uUAGCugGUAa-----------AGAAGGUAGugGGCC- -5'
miRNA: 3'- -UUAGCUGguaaAGaAGGUAGUGGGCC- -5'
miRNA: 3'- -UUAGCUGGUAAAGAAGGUAGUGGGCC- -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 | |||||||
| 21762 | 3' | -49.4 | NC_004813.1 | + | 25761 | 0.66 | 0.962562 |
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Target: 5'- uGGUUG-CCAUUUUcuuUUCCAcCGCCUGGc -3' miRNA: 3'- -UUAGCuGGUAAAG---AAGGUaGUGGGCC- -5' |
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| 21762 | 3' | -49.4 | NC_004813.1 | + | 29033 | 0.69 | 0.872755 |
|
Target: 5'- gGAUUGACCAUggcgaggUUUUCCAUCAgcaggugagcCCCGc -3' miRNA: 3'- -UUAGCUGGUAa------AGAAGGUAGU----------GGGCc -5' |
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| 21762 | 3' | -49.4 | NC_004813.1 | + | 20267 | 0.71 | 0.797719 |
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Target: 5'- uAUUGugCGUaaucccacggacUCUUCCAUCugCCGGa -3' miRNA: 3'- uUAGCugGUAa-----------AGAAGGUAGugGGCC- -5' |
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| 21762 | 3' | -49.4 | NC_004813.1 | + | 41194 | 0.72 | 0.714715 |
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Target: 5'- gGGUUGAC----UCaUCCGUCACCCGGa -3' miRNA: 3'- -UUAGCUGguaaAGaAGGUAGUGGGCC- -5' |
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| 21762 | 3' | -49.4 | NC_004813.1 | + | 12924 | 1.1 | 0.003645 |
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Target: 5'- gAAUCGACCAUUUCUUCCAUCACCCGGg -3' miRNA: 3'- -UUAGCUGGUAAAGAAGGUAGUGGGCC- -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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