miRNA: 3'- -GCGUUAGCuGGGAUUGCGcGUGGACu -5'
miRNA: 3'- -GCGUUAGCUG--------GGA---UUGCGCG-------UGGACU- -5'
miRNA: 3'- -GCGUUAGCUGGGAUUGCGCGUGGACU- -5'
Results 21 - 23 of 23 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 | |||||||
| 12428 | 3' | -53.8 | NC_003324.1 | + | 48378 | 0.71 | 0.499782 |
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Target: 5'- uCGCAGUUGcCCUUGGCGCcUACCUGc -3' miRNA: 3'- -GCGUUAGCuGGGAUUGCGcGUGGACu -5' |
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| 12428 | 3' | -53.8 | NC_003324.1 | + | 31039 | 0.72 | 0.447964 |
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Target: 5'- gCGCGGUCGGCguucaacuCCUgcuGACGCGCugcgacgGCCUGAu -3' miRNA: 3'- -GCGUUAGCUG--------GGA---UUGCGCG-------UGGACU- -5' |
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| 12428 | 3' | -53.8 | NC_003324.1 | + | 11417 | 1.1 | 0.001363 |
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Target: 5'- aCGCAAUCGACCCUAACGCGCACCUGAu -3' miRNA: 3'- -GCGUUAGCUGGGAUUGCGCGUGGACU- -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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