miRNA: 3'- gUCG--UGAGGUCCUUAGCUAAuAguAG- -5'
miRNA: 3'- -GUCGUGAGG---------UCCUUAGCUaaUAgUAG- -5'
miRNA: 3'- -GUCGUGa--------GGUCCuu-AGCUAAuAGUAG- -5'
miRNA: 3'- -GUCGUGAGGUCCUUAGCUAAUAGUAG- -5'
Results 1 - 4 of 4 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 | |||||||
| 22832 | 3' | -47.4 | NC_005135.1 | + | 23115 | 0.66 | 0.999905 |
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Target: 5'- uGGCcaACUUCAGGAGUUGGUUcUguUCu -3' miRNA: 3'- gUCG--UGAGGUCCUUAGCUAAuAguAG- -5' |
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| 22832 | 3' | -47.4 | NC_005135.1 | + | 16571 | 0.68 | 0.998983 |
|
Target: 5'- cCAGCAUUCUgaaugaaaaGGGAGUCGA--GUgGUCc -3' miRNA: 3'- -GUCGUGAGG---------UCCUUAGCUaaUAgUAG- -5' |
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| 22832 | 3' | -47.4 | NC_005135.1 | + | 7072 | 0.69 | 0.996312 |
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Target: 5'- uUAGCACgcucaauugCCAGGuucUCGAUU-UCAUCg -3' miRNA: 3'- -GUCGUGa--------GGUCCuu-AGCUAAuAGUAG- -5' |
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| 22832 | 3' | -47.4 | NC_005135.1 | + | 53521 | 1.1 | 0.017435 |
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Target: 5'- uCAGCACUCCAGGAAUCGAUUAUCAUCu -3' miRNA: 3'- -GUCGUGAGGUCCUUAGCUAAUAGUAG- -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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