miRNA: 3'- -UUGGUCAACCGGGACUAGGUGGCGCU- -5'
miRNA: 3'- uugGUCA----ACCGGGACUa----GGUGgCGCU- -5'
miRNA: 3'- -UUGGuCAACCGGgACUAGg-UGGCgCU- -5'
miRNA: 3'- -UUGGUCAACCGG-GACU--------------AGGUGGCGcu -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 | |||||||
| 32297 | 3' | -57.8 | NC_007024.1 | + | 2238 | 1.06 | 0.000792 |
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Target: 5'- cAACCAGUUGGCCCUGAUCCACCGCGAu -3' miRNA: 3'- -UUGGUCAACCGGGACUAGGUGGCGCU- -5' |
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| 32297 | 3' | -57.8 | NC_007024.1 | + | 30206 | 0.69 | 0.354019 |
|
Target: 5'- --aCAGUguucUGGCCCUGAcgaggCCAUgGCGAu -3' miRNA: 3'- uugGUCA----ACCGGGACUa----GGUGgCGCU- -5' |
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| 32297 | 3' | -57.8 | NC_007024.1 | + | 9918 | 0.67 | 0.505225 |
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Target: 5'- uAGCU-GUUGGCCgUGAUCgaACCGgGAg -3' miRNA: 3'- -UUGGuCAACCGGgACUAGg-UGGCgCU- -5' |
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| 32297 | 3' | -57.8 | NC_007024.1 | + | 27039 | 0.66 | 0.55485 |
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Target: 5'- gGAUCGGUUGGCCaCUGGcgccuuccgguguaUUCACUGCc- -3' miRNA: 3'- -UUGGUCAACCGG-GACU--------------AGGUGGCGcu -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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