miRNA: 3'- -UCCGuaUgUUCGUGAagUGGCCCCUc -5'
miRNA: 3'- uCCGUaUGUUCGUGA--------------AGUGGCCCcuc -5'
miRNA: 3'- -UCCGUAUGUU-------------CGUGAAG------UGGCCCCuc -5'
miRNA: 3'- -UCCGUAUGUUCGUGAAGUGGCCCCUC- -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 | |||||||
| 30720 | 3' | -54.2 | NC_006552.1 | + | 59633 | 0.66 | 0.783936 |
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Target: 5'- cGGGCcgGgAGGUGCUg-GCUGGGGAc -3' miRNA: 3'- -UCCGuaUgUUCGUGAagUGGCCCCUc -5' |
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| 30720 | 3' | -54.2 | NC_006552.1 | + | 10810 | 0.67 | 0.718543 |
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Target: 5'- cGGCGaACGAGUACUgcacaggcgguuguUCGCCGGGc-- -3' miRNA: 3'- uCCGUaUGUUCGUGA--------------AGUGGCCCcuc -5' |
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| 30720 | 3' | -54.2 | NC_006552.1 | + | 42301 | 0.72 | 0.4228 |
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Target: 5'- cAGGCGUGCAGaaacuccgguagcGCGCUUCuucgcuACCGGGGc- -3' miRNA: 3'- -UCCGUAUGUU-------------CGUGAAG------UGGCCCCuc -5' |
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| 30720 | 3' | -54.2 | NC_006552.1 | + | 53485 | 1.1 | 0.001231 |
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Target: 5'- gAGGCAUACAAGCACUUCACCGGGGAGg -3' miRNA: 3'- -UCCGUAUGUUCGUGAAGUGGCCCCUC- -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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