miRNA: 3'- -AGUUGAGCCGGGACUu-------GGU-CA----------AGAUG- -5'
miRNA: 3'- aGUUGAGCCGGGACUUGG----------UCaAGAUG- -5'
miRNA: 3'- -AGUUGAGCCGGGACUUGGUCAAGAUG- -5'
miRNA: 3'- -AGUUGAGCCGGGACUUGGUCAAGAUG- -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 | |||||||
| 2071 | 5' | -51.8 | NC_001348.1 | + | 102578 | 0.66 | 0.965135 |
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Target: 5'- cUCAACUCGGCCUUGGuugcaucuCCAaGUauaccuuuagUUUGCu -3' miRNA: 3'- -AGUUGAGCCGGGACUu-------GGU-CA----------AGAUG- -5' |
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| 2071 | 5' | -51.8 | NC_001348.1 | + | 104037 | 0.74 | 0.658786 |
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Target: 5'- cCGACUCGGUCCUGGGCUugguggcagaAGaUCUAUg -3' miRNA: 3'- aGUUGAGCCGGGACUUGG----------UCaAGAUG- -5' |
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| 2071 | 5' | -51.8 | NC_001348.1 | + | 122295 | 1.1 | 0.004847 |
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Target: 5'- gUCAACUCGGCCCUGAACCAGUUCUACc -3' miRNA: 3'- -AGUUGAGCCGGGACUUGGUCAAGAUG- -5' |
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| 2071 | 5' | -51.8 | NC_001348.1 | + | 107497 | 1.1 | 0.004847 |
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Target: 5'- gUCAACUCGGCCCUGAACCAGUUCUACc -3' miRNA: 3'- -AGUUGAGCCGGGACUUGGUCAAGAUG- -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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