miRNA: 3'- -GUGGUaaguCCUAGGGUCUGCGauuu -5'
miRNA: 3'- -GUGGua----AGUCCUaGGGUCUGCgaUUu -5'
miRNA: 3'- -GUGGUA-----AGUCCU--------------AGGGuCugCGAUUu -5'
miRNA: 3'- gUGGUaAGu-CCUAGGGuCUGCGAUUU- -5'
miRNA: 3'- -GUGGUAAGUCCUAGGGUCUGCGAUUU- -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 | |||||||
| 28444 | 3' | -51.4 | NC_005946.1 | + | 8791 | 0.66 | 0.966601 |
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Target: 5'- cCACCGac--GGGUCCCGGGCGUc--- -3' miRNA: 3'- -GUGGUaaguCCUAGGGUCUGCGauuu -5' |
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| 28444 | 3' | -51.4 | NC_005946.1 | + | 76351 | 0.66 | 0.959314 |
|
Target: 5'- gCGCCuggaucUCAGGG-CCCGGACGgaGAc -3' miRNA: 3'- -GUGGua----AGUCCUaGGGUCUGCgaUUu -5' |
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| 28444 | 3' | -51.4 | NC_005946.1 | + | 104084 | 0.67 | 0.945029 |
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Target: 5'- cCACCAUguugcUCAGGAucucuccugcaaacUCCCuGugGUUGAu -3' miRNA: 3'- -GUGGUA-----AGUCCU--------------AGGGuCugCGAUUu -5' |
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| 28444 | 3' | -51.4 | NC_005946.1 | + | 46988 | 0.71 | 0.799999 |
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Target: 5'- aACCAcUCuuGGAUCUCuGACGCUGGGa -3' miRNA: 3'- gUGGUaAGu-CCUAGGGuCUGCGAUUU- -5' |
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| 28444 | 3' | -51.4 | NC_005946.1 | + | 94857 | 1.06 | 0.006939 |
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Target: 5'- cCACCAUUCAGGAUCCCAGACGCUAAAc -3' miRNA: 3'- -GUGGUAAGUCCUAGGGUCUGCGAUUU- -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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