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miRNA: 3'- -CCGAUGAUGCCCUUCGUGCCCUGCAU- -5'
miRNA: 3'- cCGAUGauGCCCuUCGUGCCCuGCau -5'
miRNA: 3'- cCGaUGa----UGCCCU-----UCGUGCCCUGCau -5'
miRNA: 3'- -CCGaUGAUGCCCU------------UCGUGC--CCUGcau -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 22038 | 5' | -55.1 | NC_004927.1 | + | 16443 | 1.09 | 0.001659 |
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Target: 5'- gGGCUACUACGGGAAGCACGGGACGUAu -3' miRNA: 3'- -CCGAUGAUGCCCUUCGUGCCCUGCAU- -5' |
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| 22038 | 5' | -55.1 | NC_004927.1 | + | 61480 | 0.68 | 0.672534 |
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Target: 5'- cGCUACggUGGGuAGCACGGG-CGa- -3' miRNA: 3'- cCGAUGauGCCCuUCGUGCCCuGCau -5' |
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| 22038 | 5' | -55.1 | NC_004927.1 | + | 65810 | 0.67 | 0.766271 |
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Target: 5'- cGCgACaugaaGCGGGAuuuuaAGCGCGGGAUGg- -3' miRNA: 3'- cCGaUGa----UGCCCU-----UCGUGCCCUGCau -5' |
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| 22038 | 5' | -55.1 | NC_004927.1 | + | 40480 | 0.66 | 0.78592 |
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Target: 5'- cGGCaACUACGGGAagaaucccgacaAGUACGaaGGACu-- -3' miRNA: 3'- -CCGaUGAUGCCCU------------UCGUGC--CCUGcau -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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