miRNA: 3'- cAGCGCGUgcuaGCGCA---UCGUCAGCa -5'
miRNA: 3'- caGCGCGUGCU-----------AGCGCau-------------CGUCAGCa -5'
miRNA: 3'- -CAGCGcGUGCuAGCGCaUCGUCa--GCA- -5'
miRNA: 3'- caGCGCGUGCUAGC--GCA-------------UCGUCA---GCA- -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
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R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 24839 | 3' | -55.7 | NC_005284.1 | + | 11340 | 0.72 | 0.363753 |
|
Target: 5'- aUCGCGCAacugCGCGUcgaGGCGGUCGc -3' miRNA: 3'- cAGCGCGUgcuaGCGCA---UCGUCAGCa -5' |
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| 24839 | 3' | -55.7 | NC_005284.1 | + | 10390 | 0.67 | 0.622359 |
|
Target: 5'- -cUGCGCACGAagcaagaggcgUCGCGggcggccgaugacgcGCAGUCGg -3' miRNA: 3'- caGCGCGUGCU-----------AGCGCau-------------CGUCAGCa -5' |
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| 24839 | 3' | -55.7 | NC_005284.1 | + | 9915 | 0.69 | 0.496789 |
|
Target: 5'- cGUCGCuCGCGcUCGCGcAGCAGcggCGUa -3' miRNA: 3'- -CAGCGcGUGCuAGCGCaUCGUCa--GCA- -5' |
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| 24839 | 3' | -55.7 | NC_005284.1 | + | 6848 | 0.67 | 0.646514 |
|
Target: 5'- -gCGCGCGCGAUCGauCGUgugcucggagggcGGCGGUgagCGUg -3' miRNA: 3'- caGCGCGUGCUAGC--GCA-------------UCGUCA---GCA- -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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