miRNA: 3'- ggCCGCGACCGCU------------GAC-GUAGuCGGUA- -5'
miRNA: 3'- -GGCCGCGACCG-----------CUGACGU---------------AGUCGGua -5'
miRNA: 3'- ggCCGCG---------ACCGCuGACGUA-----------GUCGGUA- -5'
miRNA: 3'- -GGCCGCGACCGCUGACGUAGUCGGUA- -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 | |||||||
| 27262 | 3' | -59.6 | NC_005841.1 | + | 2693 | 0.66 | 0.370802 |
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Target: 5'- -aGGCGCUGGCGAacuuuuccgguuUUGuUAUC-GCCGUa -3' miRNA: 3'- ggCCGCGACCGCU------------GAC-GUAGuCGGUA- -5' |
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| 27262 | 3' | -59.6 | NC_005841.1 | + | 30709 | 0.67 | 0.348522 |
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Target: 5'- aUCGGUGUUGGCcugccuggucaGACUGCGuaacuaacaggggcuUCGGCCc- -3' miRNA: 3'- -GGCCGCGACCG-----------CUGACGU---------------AGUCGGua -5' |
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| 27262 | 3' | -59.6 | NC_005841.1 | + | 32419 | 0.67 | 0.34518 |
|
Target: 5'- -aGGCGCaaccaccguUGGCG-CUGCGUuguaugucgcgCAGCCAUc -3' miRNA: 3'- ggCCGCG---------ACCGCuGACGUA-----------GUCGGUA- -5' |
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| 27262 | 3' | -59.6 | NC_005841.1 | + | 36878 | 1.07 | 0.000333 |
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Target: 5'- cCCGGCGCUGGCGACUGCAUCAGCCAUu -3' miRNA: 3'- -GGCCGCGACCGCUGACGUAGUCGGUA- -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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