miRNA: 3'- -GCGUG-GUCG---CUCUUCuuag-CCCCGUg -5'
miRNA: 3'- gCgUGG--UCGC-UCUUCUuaGCCCCGUg -5'
miRNA: 3'- gCG-UGGUCGCUCUu----C------------UUAGCCCCGUg -5'
miRNA: 3'- -GCGUGGUCGCUCUUCUUAGCCCCGUG- -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 | |||||||
| 15440 | 3' | -56 | NC_003930.1 | + | 10681 | 0.66 | 0.26085 |
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Target: 5'- aCGCAUgCAGCguaGAGAGGucagaGGGGCAg -3' miRNA: 3'- -GCGUG-GUCG---CUCUUCuuag-CCCCGUg -5' |
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| 15440 | 3' | -56 | NC_003930.1 | + | 1687 | 0.66 | 0.253442 |
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Target: 5'- uGgACCucGGCGaAGAAGA--CGGGGCGg -3' miRNA: 3'- gCgUGG--UCGC-UCUUCUuaGCCCCGUg -5' |
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| 15440 | 3' | -56 | NC_003930.1 | + | 9052 | 0.66 | 0.232253 |
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Target: 5'- gGCuAUCGGCGAGAuacacGcuguuccgucacAAUCGGGGCAg -3' miRNA: 3'- gCG-UGGUCGCUCUu----C------------UUAGCCCCGUg -5' |
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| 15440 | 3' | -56 | NC_003930.1 | + | 260 | 1.09 | 0.000093 |
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Target: 5'- gCGCACCAGCGAGAAGAAUCGGGGCACc -3' miRNA: 3'- -GCGUGGUCGCUCUUCUUAGCCCCGUG- -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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