miRNA: 3'- gcuCCUCCAG---ACG-----ACCUAGCUCU------ACG- -5'
miRNA: 3'- gCUCCUCCaGACGA-----------CCUAgCUCuaCG- -5'
miRNA: 3'- -GCUCCU-CCaGACGACCUAGcUCUACg -5'
miRNA: 3'- -GCUCCUCCAGACGACCUAGCUCUACG- -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 | |||||||
| 11848 | 5' | -54.2 | NC_003266.2 | + | 10521 | 0.66 | 0.661068 |
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Target: 5'- --uGGAGGUUuugUGCaggccUGGGUCGAGAcgggagUGCc -3' miRNA: 3'- gcuCCUCCAG---ACG-----ACCUAGCUCU------ACG- -5' |
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| 11848 | 5' | -54.2 | NC_003266.2 | + | 10848 | 0.69 | 0.503986 |
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Target: 5'- gGAGGGGG-CUGCUguugcgguggaGGGUgGGGgcGCa -3' miRNA: 3'- gCUCCUCCaGACGA-----------CCUAgCUCuaCG- -5' |
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| 11848 | 5' | -54.2 | NC_003266.2 | + | 9848 | 0.79 | 0.112976 |
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Target: 5'- gCGAGGAuGGcCUGCUGGAUCuGGGUGa -3' miRNA: 3'- -GCUCCU-CCaGACGACCUAGcUCUACg -5' |
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| 11848 | 5' | -54.2 | NC_003266.2 | + | 5094 | 1.12 | 0.000497 |
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Target: 5'- aCGAGGAGGUCUGCUGGAUCGAGAUGCc -3' miRNA: 3'- -GCUCCUCCAGACGACCUAGCUCUACG- -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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