miRNA: 3'- -CUGACGGua-------GGACUa-CCGGA-CGCaag -5'
miRNA: 3'- cUGACGGUa-----GGa---CUACCGGaC-GCAAG- -5'
miRNA: 3'- -CUGACGGUaGGaCuaCCGGACG--------CAAG- -5'
miRNA: 3'- -CUGaCG--GUAGGACUACCGGAcGCaAG- -5'
miRNA: 3'- -CUGACGGUAGGACUACCGGACGCAAG- -5'
Results 1 - 5 of 5 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 | |||||||
| 27028 | 3' | -55.7 | NC_005832.1 | + | 32104 | 0.66 | 0.79187 |
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Target: 5'- gGACUGCCugugcggggCCUGAaaGGCCUcGCGg-- -3' miRNA: 3'- -CUGACGGua-------GGACUa-CCGGA-CGCaag -5' |
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| 27028 | 3' | -55.7 | NC_005832.1 | + | 35085 | 0.69 | 0.659188 |
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Target: 5'- uGCUGCCAcgagugCCccggGAUGGCCgGaCGUUCu -3' miRNA: 3'- cUGACGGUa-----GGa---CUACCGGaC-GCAAG- -5' |
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| 27028 | 3' | -55.7 | NC_005832.1 | + | 13046 | 0.69 | 0.648534 |
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Target: 5'- cGGCUGCCAgCUcGggGGCCUGCucgccuccGUUCu -3' miRNA: 3'- -CUGACGGUaGGaCuaCCGGACG--------CAAG- -5' |
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| 27028 | 3' | -55.7 | NC_005832.1 | + | 29664 | 0.69 | 0.648534 |
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Target: 5'- aGACcGUcuCAUCCUGGUGGCCUcCGcUCa -3' miRNA: 3'- -CUGaCG--GUAGGACUACCGGAcGCaAG- -5' |
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| 27028 | 3' | -55.7 | NC_005832.1 | + | 9648 | 1.1 | 0.001321 |
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Target: 5'- cGACUGCCAUCCUGAUGGCCUGCGUUCa -3' miRNA: 3'- -CUGACGGUAGGACUACCGGACGCAAG- -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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