miRNA: 3'- -GGUAGGuCAACAuGUCC----------CGUGUGUcu -5'
miRNA: 3'- -GGUAGgUCAacauGUCCCGUgUGUCu -5'
miRNA: 3'- gGUAGGU-CaaCAUGUCCCG---UGUGUcu -5'
miRNA: 3'- -GGU---AGGuCA---ACA---UGUCCCGUgUGUCU- -5'
miRNA: 3'- -GGUAGGUCAACAUGUCCCGUGUGUCU- -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 | |||||||
| 28421 | 5' | -51.4 | NC_005946.1 | + | 9703 | 0.66 | 0.967806 |
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Target: 5'- gCCAUCCuGUUGU-CGGGggugagugcgGCGCACGu- -3' miRNA: 3'- -GGUAGGuCAACAuGUCC----------CGUGUGUcu -5' |
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| 28421 | 5' | -51.4 | NC_005946.1 | + | 101291 | 0.68 | 0.938969 |
|
Target: 5'- gCCAUCgAGUac--CAGGGCAgGCAGc -3' miRNA: 3'- -GGUAGgUCAacauGUCCCGUgUGUCu -5' |
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| 28421 | 5' | -51.4 | NC_005946.1 | + | 102308 | 0.68 | 0.922703 |
|
Target: 5'- aCGUCCAcGccGUGCAGGGCcccGCACGc- -3' miRNA: 3'- gGUAGGU-CaaCAUGUCCCG---UGUGUcu -5' |
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| 28421 | 5' | -51.4 | NC_005946.1 | + | 76770 | 0.71 | 0.807284 |
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Target: 5'- cCCAuauUCCuGUcuaUGUucgGCAGGGCAgGCAGGa -3' miRNA: 3'- -GGU---AGGuCA---ACA---UGUCCCGUgUGUCU- -5' |
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| 28421 | 5' | -51.4 | NC_005946.1 | + | 79115 | 1.12 | 0.003406 |
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Target: 5'- cCCAUCCAGUUGUACAGGGCACACAGAa -3' miRNA: 3'- -GGUAGGUCAACAUGUCCCGUGUGUCU- -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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