miRNA: 3'- gAGGACCGcCAGaaauGCAGCCCcug -5'
miRNA: 3'- gaGGACCGCCAGaaa----UG-Ca---GCCCCUG- -5'
miRNA: 3'- gAGGACC-GCC--------------AGAAaUGCAGCC-CCUG- -5'
miRNA: 3'- gaGGACCGCCAgAaa-UGCAG----CCCCUg -5'
miRNA: 3'- -GAGGACCGCCAGAAAUGCAGCCCCUG- -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 | |||||||
| 28387 | 5' | -56.3 | NC_005946.1 | + | 100022 | 0.66 | 0.834005 |
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Target: 5'- gUCCUGGCaGUUgu--CGUCGGGa-- -3' miRNA: 3'- gAGGACCGcCAGaaauGCAGCCCcug -5' |
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| 28387 | 5' | -56.3 | NC_005946.1 | + | 13682 | 0.66 | 0.834005 |
|
Target: 5'- -cCCUGGCGGUCaugccagACaGgaggUGGGGAUc -3' miRNA: 3'- gaGGACCGCCAGaaa----UG-Ca---GCCCCUG- -5' |
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| 28387 | 5' | -56.3 | NC_005946.1 | + | 17736 | 0.67 | 0.777382 |
|
Target: 5'- uUCCUGGcCGGggcacucuuucuuaUCUUgACGUUGGaGGAUg -3' miRNA: 3'- gAGGACC-GCC--------------AGAAaUGCAGCC-CCUG- -5' |
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| 28387 | 5' | -56.3 | NC_005946.1 | + | 44537 | 0.74 | 0.403331 |
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Target: 5'- -cCCUGGCGGUgUgagGCGUCuugaGGGGAg -3' miRNA: 3'- gaGGACCGCCAgAaa-UGCAG----CCCCUg -5' |
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| 28387 | 5' | -56.3 | NC_005946.1 | + | 49677 | 1.09 | 0.002002 |
|
Target: 5'- cCUCCUGGCGGUCUUUACGUCGGGGACc -3' miRNA: 3'- -GAGGACCGCCAGAAAUGCAGCCCCUG- -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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