miRNA: 3'- aGCC-----UGCCGGACUUA---------UGGCuaCGCGa -5'
miRNA: 3'- -AGCC-UGCCGGacuuaUGGCUAC-GCGa -5'
miRNA: 3'- -AGCCuGCCGGACuuau---GGCUA---CGCGa -5'
miRNA: 3'- aGCCUGCCGgacuuaUGGCUa--CGCGa -5'
miRNA: 3'- aGCCU--GCCGGacUUAUGGCUaCGCGa -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 28013 | 3' | -55.6 | NC_005887.1 | + | 20866 | 0.67 | 0.526293 |
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Target: 5'- aCGGuguugGCGGCCUGAAUgauaguggcGCCGgcGUGUc -3' miRNA: 3'- aGCC-----UGCCGGACUUA---------UGGCuaCGCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 17744 | 0.69 | 0.463397 |
|
Target: 5'- cUCGGcACGGCCgcgcgGCUGAUGgCGCc -3' miRNA: 3'- -AGCC-UGCCGGacuuaUGGCUAC-GCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 10925 | 0.69 | 0.453294 |
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Target: 5'- gUCGGcCGGCCUGcucacgcCCGAUuacGCGCa -3' miRNA: 3'- -AGCCuGCCGGACuuau---GGCUA---CGCGa -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 | + | 27749 | 0.69 | 0.414127 |
|
Target: 5'- aCGGAagUGGCC--GAUGCCGA-GCGCg -3' miRNA: 3'- aGCCU--GCCGGacUUAUGGCUaCGCGa -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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