miRNA: 3'- caaACCAAU---GA--AugCUUGCGG--CUCCA- -5'
miRNA: 3'- -CAAACCAa--UGaau-----GCuUGCGGCUCCa -5'
miRNA: 3'- caaaccaAUGaAUGCU--UGCGGCUCCA- -5'
miRNA: 3'- -CAAACCAAUGAAUGCUUGCGGCUCCA- -5'
Results 1 - 4 of 4 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 | |||||||
| 11321 | 3' | -48.2 | NC_003084.1 | + | 11886 | 0.66 | 0.997969 |
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Target: 5'- --aUGGUUGggcCUucUugGAACGCUuuGAGGUa -3' miRNA: 3'- caaACCAAU---GA--AugCUUGCGG--CUCCA- -5' |
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| 11321 | 3' | -48.2 | NC_003084.1 | + | 98358 | 0.66 | 0.997083 |
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Target: 5'- cGUUUGGUgccACcaacauccCGcGCGCCGAGGa -3' miRNA: 3'- -CAAACCAa--UGaau-----GCuUGCGGCUCCa -5' |
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| 11321 | 3' | -48.2 | NC_003084.1 | + | 88844 | 0.68 | 0.989831 |
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Target: 5'- ------cUAC-UACGAgaGCGCCGAGGUg -3' miRNA: 3'- caaaccaAUGaAUGCU--UGCGGCUCCA- -5' |
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| 11321 | 3' | -48.2 | NC_003084.1 | + | 26136 | 1.07 | 0.014549 |
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Target: 5'- gGUUUGGUUACUUACGAACGCCGAGGUc -3' miRNA: 3'- -CAAACCAAUGAAUGCUUGCGGCUCCA- -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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