miRNA: 3'- -AGCCuGCCGGACuuau---GGCUA---CGCGa -5'
miRNA: 3'- aGCCUGcCGG--ACUUaUGGCuaCGCGa -5'
miRNA: 3'- aGCCUGCCGGa----CUUaUGGCU--ACGCGa -5'
miRNA: 3'- aGCCUGCCGgacuuaUGGCUa--CGCGa -5'
miRNA: 3'- -AGCC-UGC-----------CGGACuu-AUGGCUACGCGa -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 28013 | 3' | -55.6 | NC_005887.1 | + | 10925 | 0.69 | 0.453294 |
|
Target: 5'- gUCGGcCGGCCUGcucacgcCCGAUuacGCGCa -3' miRNA: 3'- -AGCCuGCCGGACuuau---GGCUA---CGCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 8846 | 0.66 | 0.614443 |
|
Target: 5'- gCGGGCaGCUugUGAAcGCCGgcGCGCc -3' miRNA: 3'- aGCCUGcCGG--ACUUaUGGCuaCGCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 6435 | 0.73 | 0.27294 |
|
Target: 5'- cCGGACGGCCgcgccGAG-AUCGAagUGCGCg -3' miRNA: 3'- aGCCUGCCGGa----CUUaUGGCU--ACGCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 2702 | 0.69 | 0.423724 |
|
Target: 5'- aCGGGCGGCaagcg-GCCGAgccGCGCg -3' miRNA: 3'- aGCCUGCCGgacuuaUGGCUa--CGCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 1709 | 0.71 | 0.359459 |
|
Target: 5'- aUCGGcGCGcgcucgucaguGCCUGucuUGCCGAUGUGCg -3' miRNA: 3'- -AGCC-UGC-----------CGGACuu-AUGGCUACGCGa -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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