miRNA: 3'- -GGCAG-GUAUAG-----UCGUGag-UGGGACGa -5'
miRNA: 3'- ggcaGGUaUAGUCGUgAGUGGgACGa -5'
miRNA: 3'- -GGCAGGUA-------UAGuC-GUGAG---------UGGGACGa -5'
miRNA: 3'- gGCAGGUauAGUCGUGA----GUGGGACGA- -5'
miRNA: 3'- -GGCAGGUAUAGUCGUGAGUGGGACGA- -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 | |||||||
| 21887 | 5' | -53.7 | NC_004902.1 | + | 32622 | 0.66 | 0.754037 |
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Target: 5'- cCCGUCuUGUAUUgcccuGGCACagaGCCCUGCc -3' miRNA: 3'- -GGCAG-GUAUAG-----UCGUGag-UGGGACGa -5' |
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| 21887 | 5' | -53.7 | NC_004902.1 | + | 7414 | 0.67 | 0.643323 |
|
Target: 5'- ---aCCGaGUCAGCAgUCGCCgUGCg -3' miRNA: 3'- ggcaGGUaUAGUCGUgAGUGGgACGa -5' |
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| 21887 | 5' | -53.7 | NC_004902.1 | + | 33361 | 0.68 | 0.630866 |
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Target: 5'- gUCGUCCAUgcuggcaAUCuGcCACUCcugggccauGCCCUGCa -3' miRNA: 3'- -GGCAGGUA-------UAGuC-GUGAG---------UGGGACGa -5' |
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| 21887 | 5' | -53.7 | NC_004902.1 | + | 25544 | 0.71 | 0.427055 |
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Target: 5'- uUGUCCAgcUCAGUGCUggugCGCCUUGCUu -3' miRNA: 3'- gGCAGGUauAGUCGUGA----GUGGGACGA- -5' |
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| 21887 | 5' | -53.7 | NC_004902.1 | + | 26003 | 1.1 | 0.000867 |
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Target: 5'- gCCGUCCAUAUCAGCACUCACCCUGCUg -3' miRNA: 3'- -GGCAGGUAUAGUCGUGAGUGGGACGA- -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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