miRNA: 3'- aaAGAUCUAUuuUUCGCa-----------UGGGGCaa -5'
miRNA: 3'- aAAGA---------------UCUA---UUUUUCGCAUGGGGcaa -5'
miRNA: 3'- aaAGa---UCUAuuUUUCGCAUGGGGCaa -5'
miRNA: 3'- aaagaucuaUUUUUCGCAUGGGGCAA- -5'
miRNA: 3'- -AAAGAUCUAUUUUUCGCAUGGGGCAA- -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 | |||||||
| 25939 | 3' | -45.8 | NC_005337.1 | + | 85536 | 0.69 | 0.997066 |
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Target: 5'- -gUCUGGAUGuuGAGCGcggcggugagaaGCCCCGg- -3' miRNA: 3'- aaAGAUCUAUuuUUCGCa-----------UGGGGCaa -5' |
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| 25939 | 3' | -45.8 | NC_005337.1 | + | 95033 | 0.7 | 0.994753 |
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Target: 5'- gUUCUucacguacaccucgcGGAUugcGAAGAGCGUGCCCCc-- -3' miRNA: 3'- aAAGA---------------UCUA---UUUUUCGCAUGGGGcaa -5' |
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| 25939 | 3' | -45.8 | NC_005337.1 | + | 32217 | 0.71 | 0.988249 |
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Target: 5'- -cUCgaagAGGUcgGAGGCGUGCUCCGg- -3' miRNA: 3'- aaAGa---UCUAuuUUUCGCAUGGGGCaa -5' |
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| 25939 | 3' | -45.8 | NC_005337.1 | + | 17280 | 0.74 | 0.933547 |
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Target: 5'- --------aAAAAAGCGUACCCCGUUg -3' miRNA: 3'- aaagaucuaUUUUUCGCAUGGGGCAA- -5' |
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| 25939 | 3' | -45.8 | NC_005337.1 | + | 116963 | 1.04 | 0.039851 |
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Target: 5'- cUUUCUAGAUAAAAAGCGUACCCCGUUg -3' miRNA: 3'- -AAAGAUCUAUUUUUCGCAUGGGGCAA- -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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