miRNA: 3'- uuauUCGGuaa-AUGGUCGACCA----UCGu -5'
miRNA: 3'- uuaUUCgGUAAAUGGUC-GACCAUCgu -5'
miRNA: 3'- uuaUUCGGUAAAUGGUC--GACCAUCGu -5'
miRNA: 3'- uUAUUCGGUAaa-UGGUCG----------ACCAUCGu -5'
miRNA: 3'- -UUAUUCGGUAAAUGGUCGACCAUCGU- -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 | |||||||
| 31570 | 3' | -48.3 | NC_006852.1 | + | 2208 | 0.66 | 0.883815 |
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Target: 5'- ---uGGCUuugcUACCAGCUGGUaaauGGCu -3' miRNA: 3'- uuauUCGGuaa-AUGGUCGACCA----UCGu -5' |
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| 31570 | 3' | -48.3 | NC_006852.1 | + | 4345 | 0.66 | 0.847495 |
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Target: 5'- --cAGGgCGUUUGCCAGgUUGGUGGa- -3' miRNA: 3'- uuaUUCgGUAAAUGGUC-GACCAUCgu -5' |
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| 31570 | 3' | -48.3 | NC_006852.1 | + | 29430 | 0.68 | 0.784674 |
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Target: 5'- --cAGGUUGUUUAUCAGgaCUGGUAGCu -3' miRNA: 3'- uuaUUCGGUAAAUGGUC--GACCAUCGu -5' |
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| 31570 | 3' | -48.3 | NC_006852.1 | + | 28796 | 0.68 | 0.761956 |
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Target: 5'- cGUAGGCCGUgaaGCUAGUaaugaauuuuUGGUGGCc -3' miRNA: 3'- uUAUUCGGUAaa-UGGUCG----------ACCAUCGu -5' |
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| 31570 | 3' | -48.3 | NC_006852.1 | + | 2271 | 1.07 | 0.002342 |
|
Target: 5'- aAAUAAGCCAUUUACCAGCUGGUAGCAa -3' miRNA: 3'- -UUAUUCGGUAAAUGGUCGACCAUCGU- -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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